rs10999637

Variant names:

• chr10-71019055-G-A
• rs10999637
• ENST00000646051.1:n.259-7524G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646051.1(ENSG00000285300):​n.259-7524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,236 control chromosomes in the GnomAD database, including 52,879 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 0.83 (52879 hom., cov: 33)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.859 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
ENSG00000285300	ENST00000646051.1	n.259-7524G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126523 AN: 152118 Hom.: 52835 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.832 AC: 126623 AN: 152236 Hom.: 52879 Cov.: 33 AF XY: 0.829 AC XY: 61678 AN XY: 74422

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.852

Alfa AF: 0.833 Hom.: 8308

Bravo AF: 0.824

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10999637; hg19: chr10-72778812;