rs1334806

Variant names:

• chr1-62409642-A-G
• rs1334806

Your query was ambiguous. Multiple possible variants found:

• chr1-62409642-A-G
• chr1-62409642-A-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 0.795 in 152,128 control chromosomes in the GnomAD database, including 48,508 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 0.80 (48508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 9 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 = 0.875 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: 0.795 AC: 120827 AN: 152008 Hom.: 48448 Cov.: 31

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.795 AC: 120950 AN: 152128 Hom.: 48508 Cov.: 31 AF XY: 0.799 AC XY: 59390 AN XY: 74374

African (AFR) AF: 0.882 AC: 36632 AN: 41510

American (AMR) AF: 0.812 AC: 12424 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2922 AN: 5156

South Asian (SAS) AF: 0.834 AC: 4019 AN: 4818

European-Finnish (FIN) AF: 0.818 AC: 8652 AN: 10582

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

European-Non Finnish (NFE) AF: 0.754 AC: 51237 AN: 67986

Other (OTH) AF: 0.800 AC: 1684 AN: 2106

Alfa AF: 0.771 Hom.: 78758

Bravo AF: 0.797

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.59
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1334806; hg19: chr1-62875313;