1-30572662-A-G

Variant names:

• chr1-30572662-A-G
• rs3104435

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 0.795 in 152,172 control chromosomes in the GnomAD database, including 48,139 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 0.79 (48139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.794 AC: 120796 AN: 152054 Hom.: 48089 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.795 AC: 120901 AN: 152172 Hom.: 48139 Cov.: 32 AF XY: 0.794 AC XY: 59060 AN XY: 74392

African (AFR) AF: 0.826 AC: 34287 AN: 41520

American (AMR) AF: 0.773 AC: 11813 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2669 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4003 AN: 5166

South Asian (SAS) AF: 0.700 AC: 3368 AN: 4810

European-Finnish (FIN) AF: 0.809 AC: 8580 AN: 10604

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53657 AN: 67998

Other (OTH) AF: 0.775 AC: 1636 AN: 2112

Alfa AF: 0.788 Hom.: 203798

Bravo AF: 0.796

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs3104435; hg19: chr1-31045509; COSMIC: COSV59935777;