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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421629.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229672	ENST00000421629.2	TSL:3	n.551-953G>A		intron	N/A
	ENSG00000229672	ENST00000661014.1		n.209-953G>A		intron	N/A
	ENSG00000229672	ENST00000796007.1		n.156-953G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10508264;

hg19: chr10-3804257;