rs1009080

chr1-29958713-G-Achr1-29958713-G-Cchr1-29958713-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.568

Alfa AF: 0.669 Hom.: 75645

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

Splicing

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

Publications

LitVar

Other links and lift over

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