rs10510962

Variant names:

• chr3-66989016-G-A
• rs10510962
• ENST00000780190.1:n.114+1210C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-66989016-G-A
• chr3-66989016-G-C

Variant summary

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

The ENST00000780190.1(ENSG00000301618):​n.114+1210C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,220 control chromosomes in the GnomAD database, including 504 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 0.046 (504 hom., cov: 33)
• Consequence: ENSG00000301618 ENST00000780190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 0 publications found

Genes affected

ENSG00000301618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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
ENSG00000301618	ENST00000780190.1	n.114+1210C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7038 AN: 152102 Hom.: 503 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00463

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0463 AC: 7053 AN: 152220 Hom.: 504 Cov.: 33 AF XY: 0.0451 AC XY: 3356 AN XY: 74426

African (AFR) AF: 0.153 AC: 6366 AN: 41494

American (AMR) AF: 0.0175 AC: 268 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4826

European-Finnish (FIN) AF: 0.000754 AC: 8 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00463 AC: 315 AN: 68022

Other (OTH) AF: 0.0364 AC: 77 AN: 2116

Alfa AF: 0.0612 Hom.: 247

Bravo AF: 0.0526

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.53
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10510962; hg19: chr3-67039440;