rs10489741

Variant names:

• chr1-96476850-G-A
• rs10489741

Your query was ambiguous. Multiple possible variants found:

• chr1-96476850-G-A
• chr1-96476850-G-C
• chr1-96476850-G-T

Variant summary

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

The variant allele was found at a frequency of 0.553 in 152,078 control chromosomes in the GnomAD database, including 23,933 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 0.55 (23933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84045 AN: 151962 Hom.: 23932 Cov.: 33

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.553 AC: 84072 AN: 152078 Hom.: 23933 Cov.: 33 AF XY: 0.553 AC XY: 41077 AN XY: 74336

African (AFR) AF: 0.432 AC: 17898 AN: 41470

American (AMR) AF: 0.583 AC: 8922 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4572 AN: 5170

South Asian (SAS) AF: 0.504 AC: 2432 AN: 4824

European-Finnish (FIN) AF: 0.597 AC: 6302 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40275 AN: 67982

Other (OTH) AF: 0.545 AC: 1152 AN: 2114

Alfa AF: 0.578 Hom.: 108278

Bravo AF: 0.549

Asia WGS AF: 0.705 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs10489741; hg19: chr1-96942406;