rs10508264

Variant names:

• chr10-3762065-G-A
• rs10508264
• ENST00000421629.2:n.551-953G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-3762065-G-A
• chr10-3762065-G-C

Variant summary

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

The ENST00000421629.2(ENSG00000229672):​n.551-953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,234 control chromosomes in the GnomAD database, including 874 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 0.093 (874 hom., cov: 32)
• Consequence: ENSG00000229672 ENST00000421629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 7 publications found

Genes affected

ENSG00000229672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376363	XR_001747332.1	n.190-953G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229672	ENST00000421629.2	n.551-953G>A		intron_variant	Intron 5 of 5	3
ENSG00000229672	ENST00000661014.1	n.209-953G>A		intron_variant	Intron 2 of 2
ENSG00000229672	ENST00000796007.1	n.156-953G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14227 AN: 152116 Hom.: 874 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0935 AC: 14227 AN: 152234 Hom.: 874 Cov.: 32 AF XY: 0.0960 AC XY: 7144 AN XY: 74392

African (AFR) AF: 0.0249 AC: 1033 AN: 41568

American (AMR) AF: 0.100 AC: 1536 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5178

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4830

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10564

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 68014

Other (OTH) AF: 0.0810 AC: 171 AN: 2110

Alfa AF: 0.107 Hom.: 1779

Bravo AF: 0.0855

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10508264; hg19: chr10-3804257;