1-62409642-A-G

Position:

• chr1-62409642-A-G

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 0.795 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.800

Alfa AF: 0.766 Hom.: 61692

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1334806; hg19: chr1-62875313;