rs151603

Variant names:

• chr10-113970222-G-A
• rs151603
• ENST00000751600.1:n.127-9478G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-113970222-G-A
• chr10-113970222-G-C
• chr10-113970222-G-T

Variant summary

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

The ENST00000751600.1(ENSG00000297898):​n.127-9478G>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 151,988 control chromosomes in the GnomAD database, including 25,591 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 (25591 hom., cov: 32)
• Consequence: ENSG00000297898 ENST00000751600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 publications found

Genes affected

ENSG00000297898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 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
ENSG00000297898	ENST00000751600.1	n.127-9478G>A		intron_variant	Intron 1 of 2
ENSG00000297898	ENST00000751601.1	n.58+3584G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86367 AN: 151870 Hom.: 25573 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.569 AC: 86430 AN: 151988 Hom.: 25591 Cov.: 32 AF XY: 0.578 AC XY: 42922 AN XY: 74296

African (AFR) AF: 0.411 AC: 17007 AN: 41422

American (AMR) AF: 0.620 AC: 9469 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5164

South Asian (SAS) AF: 0.663 AC: 3202 AN: 4826

European-Finnish (FIN) AF: 0.759 AC: 8031 AN: 10576

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.627 AC: 42612 AN: 67952

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.601 Hom.: 21223

Bravo AF: 0.548

Asia WGS AF: 0.532 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs151603; hg19: chr10-115729981;