chr2-27551835-T-G

Variant names:

• chr2-27551835-T-G
• rs2384628
• NM_032266.5:c.145-13502T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032266.5(SPATA31H1):​c.145-13502T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,216 control chromosomes in the GnomAD database, including 26,414 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (26414 hom., cov: 28)
• Consequence: SPATA31H1 NM_032266.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 8 publications found

Genes affected

SPATA31H1 (HGNC:25275): (SPATA31 subfamily H member 1) Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032266.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31H1	NM_032266.5	MANE Select	c.145-13502T>G		intron	N/A	NP_115642.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31H1	ENST00000447166.3	TSL:3 MANE Select	c.145-13502T>G		intron	N/A	ENSP00000403181.2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87418 AN: 151100 Hom.: 26367 Cov.: 28

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.599

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.579 AC: 87523 AN: 151216 Hom.: 26414 Cov.: 28 AF XY: 0.582 AC XY: 42943 AN XY: 73844

African (AFR) AF: 0.694 AC: 28436 AN: 40992

American (AMR) AF: 0.652 AC: 9901 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1945 AN: 3460

East Asian (EAS) AF: 0.855 AC: 4398 AN: 5146

South Asian (SAS) AF: 0.517 AC: 2474 AN: 4782

European-Finnish (FIN) AF: 0.498 AC: 5206 AN: 10454

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33227 AN: 67894

Other (OTH) AF: 0.599 AC: 1253 AN: 2092

Alfa AF: 0.542 Hom.: 2830

Bravo AF: 0.600

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.24
PhyloP100		-2.5

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: rs2384628; hg19: chr2-27774702; COSMIC: COSV71614025;