rs10762885

Variant names:

• chr10-52785830-G-A
• rs10762885
• ENST00000816733.1:n.505-4368G>A

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.505-4368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,668 control chromosomes in the GnomAD database, including 25,548 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 0.57 (25548 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 10 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816733.1. 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
	ENSG00000306279	ENST00000816733.1		n.505-4368G>A		intron	N/A
	ENSG00000306279	ENST00000816734.1		n.382-4368G>A		intron	N/A
	ENSG00000306279	ENST00000816735.1		n.98-4368G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86246 AN: 151552 Hom.: 25530 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.569 AC: 86312 AN: 151668 Hom.: 25548 Cov.: 31 AF XY: 0.572 AC XY: 42410 AN XY: 74112

African (AFR) AF: 0.424 AC: 17442 AN: 41172

American (AMR) AF: 0.693 AC: 10587 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3911 AN: 5120

South Asian (SAS) AF: 0.625 AC: 3004 AN: 4804

European-Finnish (FIN) AF: 0.574 AC: 6076 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40837 AN: 67928

Other (OTH) AF: 0.582 AC: 1227 AN: 2110

Alfa AF: 0.601 Hom.: 105181

Bravo AF: 0.577

Asia WGS AF: 0.700 AC: 2434 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	0.086
DANN	Benign	0.44
PhyloP100		-3.0

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: rs10762885;

hg19: chr10-54545590;