rs61732416

Variant names:

• chr9-34723342-G-A
• rs61732416
• NM_001141917.2:c.3898C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-34723342-G-A
• chr9-34723342-G-C
• chr9-34723342-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001141917.2(SPATA31F1):​c.3898C>T​(p.Arg1300Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00605 in 1,551,694 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1300G) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0035 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (33 hom.)
• Consequence: SPATA31F1 NM_001141917.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 5 publications found

Genes affected

SPATA31F1 (HGNC:41911): (SPATA31 subfamily F member 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PHF24 (HGNC:29180): (PHD finger protein 24) Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0053033233).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001141917.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31F1	NM_001141917.2	MANE Select	c.3898C>T	p.Arg1300Trp	missense	Exon 4 of 4	NP_001135389.1	Q6ZU69

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31F1	ENST00000378788.4	TSL:2 MANE Select	c.3898C>T	p.Arg1300Trp	missense	Exon 4 of 4	ENSP00000417711.1	Q6ZU69
	ENSG00000230074	ENST00000664167.1		n.86+20304G>A		intron	N/A
	ENSG00000230074	ENST00000837930.1		n.174+20304G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00356 AC: 541 AN: 152170 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00606

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00360 AC: 563 AN: 156344 AF XY: 0.00351

Gnomad AFR exome AF: 0.00189

Gnomad AMR exome AF: 0.00101

Gnomad ASJ exome AF: 0.000118

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00323

Gnomad NFE exome AF: 0.00678

Gnomad OTH exome AF: 0.00251

GnomAD4 exome AF: 0.00633 AC: 8855 AN: 1399406 Hom.: 33 Cov.: 66 AF XY: 0.00618 AC XY: 4265 AN XY: 690208

African (AFR) AF: 0.000981 AC: 31 AN: 31596

American (AMR) AF: 0.00112 AC: 40 AN: 35704

Ashkenazi Jewish (ASJ) AF: 0.0000794 AC: 2 AN: 25182

East Asian (EAS) AF: 0.0000560 AC: 2 AN: 35738

South Asian (SAS) AF: 0.00198 AC: 157 AN: 79236

European-Finnish (FIN) AF: 0.00434 AC: 214 AN: 49274

Middle Eastern (MID) AF: 0.00404 AC: 23 AN: 5698

European-Non Finnish (NFE) AF: 0.00749 AC: 8078 AN: 1078976

Other (OTH) AF: 0.00531 AC: 308 AN: 58002

GnomAD4 genome AF: 0.00355 AC: 540 AN: 152288 Hom.: 2 Cov.: 32 AF XY: 0.00329 AC XY: 245 AN XY: 74458

African (AFR) AF: 0.00156 AC: 65 AN: 41574

American (AMR) AF: 0.00118 AC: 18 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4816

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00606 AC: 412 AN: 68014

Other (OTH) AF: 0.00284 AC: 6 AN: 2114

Alfa AF: 0.00541 Hom.: 13

Bravo AF: 0.00342

TwinsUK AF: 0.00809 AC: 30

ALSPAC AF: 0.00986 AC: 38

ESP6500AA AF: 0.000723 AC: 1

ESP6500EA AF: 0.00691 AC: 22

ExAC AF: 0.00296 AC: 75

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.68	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.8
DANN	Benign	0.79
DEOGEN2	Benign	0.0018	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.029	N
LIST_S2	Benign	0.55	T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.0053	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.035	N
PhyloP100		-0.027
PrimateAI	Benign	0.21	T
PROVEAN	Benign	-0.84	N
REVEL	Benign	0.081
Sift	Benign	0.14	T
Sift4G	Benign	0.085	T
Polyphen		0.0030	B
Vest4		0.075
MVP		0.17
ClinPred		0.0014	T
GERP RS		-0.85
Varity_R		0.035
gMVP		0.073
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61732416; hg19: chr9-34723339; COSMIC: COSV105326541;