rs1009080

Variant names:

• chr1-29958713-G-A
• rs1009080

Your query was ambiguous. Multiple possible variants found:

• chr1-29958713-G-A
• chr1-29958713-G-C
• chr1-29958713-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 0.541 in 152,082 control chromosomes in the GnomAD database, including 26,025 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 0.54 (26025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.542 AC: 82333 AN: 151964 Hom.: 26025 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.541 AC: 82351 AN: 152082 Hom.: 26025 Cov.: 32 AF XY: 0.543 AC XY: 40330 AN XY: 74336

African (AFR) AF: 0.195 AC: 8077 AN: 41492

American (AMR) AF: 0.556 AC: 8497 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3713 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4816

European-Finnish (FIN) AF: 0.729 AC: 7702 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47680 AN: 67974

Other (OTH) AF: 0.568 AC: 1199 AN: 2110

Alfa AF: 0.649 Hom.: 157263

Bravo AF: 0.517

Asia WGS AF: 0.535 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1009080; hg19: chr1-30431560; COSMIC: COSV59934480;