1-62729989-C-T

Position:

• chr1-62729989-C-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 0.696 in 152,126 control chromosomes in the GnomAD database, including 39,110 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 0.70 (39110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.802 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: 0.697 AC: 105897 AN: 152008 Hom.: 39109 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.696 AC: 105919 AN: 152126 Hom.: 39110 Cov.: 33 AF XY: 0.699 AC XY: 52003 AN XY: 74384

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.737

Alfa AF: 0.773 Hom.: 23291

Bravo AF: 0.689

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6664692; hg19: chr1-63195660; COSMIC: COSV59947564;