rs10508622

Variant names:

• chr10-20409341-T-A
• rs10508622
• ENST00000785943.1:n.285+38586T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-20409341-T-A
• chr10-20409341-T-C

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.285+38586T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,186 control chromosomes in the GnomAD database, including 1,842 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 0.15 (1842 hom., cov: 32)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 1 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302338	ENST00000785943.1	n.285+38586T>A		intron_variant	Intron 1 of 5
ENSG00000302338	ENST00000785944.1	n.198+38586T>A		intron_variant	Intron 1 of 3
ENSG00000302338	ENST00000785945.1	n.132+38586T>A		intron_variant	Intron 1 of 4
ENSG00000302338	ENST00000785947.1	n.41+38586T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22703 AN: 152068 Hom.: 1833 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.149 AC: 22735 AN: 152186 Hom.: 1842 Cov.: 32 AF XY: 0.151 AC XY: 11273 AN XY: 74416

African (AFR) AF: 0.107 AC: 4443 AN: 41534

American (AMR) AF: 0.107 AC: 1637 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3470

East Asian (EAS) AF: 0.105 AC: 543 AN: 5176

South Asian (SAS) AF: 0.192 AC: 924 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10604

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.180 AC: 12247 AN: 67974

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.0866 Hom.: 128

Bravo AF: 0.139

Asia WGS AF: 0.148 AC: 515 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10508622; hg19: chr10-20698270;