rs10500980

Variant names:

• chr11-24472919-A-G
• rs10500980
• ENST00000763762.1:n.583-9555T>C

Variant summary

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

The ENST00000763762.1(ENSG00000299475):​n.583-9555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,180 control chromosomes in the GnomAD database, including 173 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 0.048 (173 hom., cov: 32)
• Consequence: ENSG00000299475 ENST00000763762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 0 publications found

Genes affected

ENSG00000299475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0573 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
ENSG00000299475	ENST00000763762.1	n.583-9555T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7303 AN: 152062 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0480 AC: 7301 AN: 152180 Hom.: 173 Cov.: 32 AF XY: 0.0481 AC XY: 3575 AN XY: 74372

African (AFR) AF: 0.0361 AC: 1501 AN: 41562

American (AMR) AF: 0.0605 AC: 924 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.0624 AC: 320 AN: 5128

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4828

European-Finnish (FIN) AF: 0.0336 AC: 357 AN: 10622

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3567 AN: 67984

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0526 Hom.: 132

Bravo AF: 0.0493

Asia WGS AF: 0.0490 AC: 170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.22
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10500980; hg19: chr11-24494465;