chr1-76714005-T-C

Position:

• chr1-76714005-T-C

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 0.682 in 151,592 control chromosomes in the GnomAD database, including 35,773 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 0.68 (35773 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 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: 0.682 AC: 103304 AN: 151474 Hom.: 35772 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.682 AC: 103332 AN: 151592 Hom.: 35773 Cov.: 31 AF XY: 0.676 AC XY: 50111 AN XY: 74082

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.690

Alfa AF: 0.733 Hom.: 54096

Bravo AF: 0.690

Asia WGS AF: 0.570 AC: 1975 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs664576; hg19: chr1-77179690;