rs10501817

Variant names:

• chr11-94961598-G-T
• rs10501817
• ENST00000765796.1:n.135+1229G>T

Variant summary

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

The ENST00000765796.1(ENSG00000299714):​n.135+1229G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,986 control chromosomes in the GnomAD database, including 19,103 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 0.50 (19103 hom., cov: 32)
• Consequence: ENSG00000299714 ENST00000765796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25
• Publications: 1 publications found

Genes affected

ENSG00000299714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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
ENSG00000299714	ENST00000765796.1	n.135+1229G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75609 AN: 151868 Hom.: 19090 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75646 AN: 151986 Hom.: 19103 Cov.: 32 AF XY: 0.495 AC XY: 36765 AN XY: 74290

African (AFR) AF: 0.493 AC: 20431 AN: 41440

American (AMR) AF: 0.457 AC: 6989 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4816

European-Finnish (FIN) AF: 0.514 AC: 5424 AN: 10550

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36022 AN: 67960

Other (OTH) AF: 0.507 AC: 1068 AN: 2106

Alfa AF: 0.522 Hom.: 4229

Bravo AF: 0.492

Asia WGS AF: 0.341 AC: 1187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0020
DANN	Benign	0.43
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs10501817; hg19: chr11-94694763;