2-27563321-A-T

Variant names:

• chr2-27563321-A-T
• rs10208529
• NM_032266.5:c.145-2016A>T

Variant summary

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

The NM_032266.5(SPATA31H1):​c.145-2016A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 141,702 control chromosomes in the GnomAD database, including 6,183 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 0.29 (6183 hom., cov: 27)
• Consequence: SPATA31H1 NM_032266.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 12 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31H1	NM_032266.5	MANE Select	c.145-2016A>T		intron	N/A	NP_115642.4	C9JG08

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31H1	ENST00000447166.3	TSL:3 MANE Select	c.145-2016A>T		intron	N/A	ENSP00000403181.2	C9JG08

Frequencies

GnomAD3 genomes AF: 0.290 AC: 41069 AN: 141636 Hom.: 6180 Cov.: 27

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.290 AC: 41080 AN: 141702 Hom.: 6183 Cov.: 27 AF XY: 0.296 AC XY: 20391 AN XY: 68822

African (AFR) AF: 0.207 AC: 7785 AN: 37556

American (AMR) AF: 0.459 AC: 6631 AN: 14432

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1171 AN: 3378

East Asian (EAS) AF: 0.505 AC: 2467 AN: 4884

South Asian (SAS) AF: 0.214 AC: 948 AN: 4432

European-Finnish (FIN) AF: 0.311 AC: 2767 AN: 8888

Middle Eastern (MID) AF: 0.366 AC: 98 AN: 268

European-Non Finnish (NFE) AF: 0.283 AC: 18372 AN: 65030

Other (OTH) AF: 0.336 AC: 666 AN: 1984

Alfa AF: 0.271 Hom.: 727

Bravo AF: 0.289

Asia WGS AF: 0.301 AC: 1049 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.4
DANN	Benign	0.55
PhyloP100		0.32

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: rs10208529; hg19: chr2-27786188;