1-63771733-G-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 0.617 in 151,978 control chromosomes in the GnomAD database, including 32,394 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 0.62 (32394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93736 AN: 151860 Hom.: 32396 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.617 AC: 93728 AN: 151978 Hom.: 32394 Cov.: 31 AF XY: 0.621 AC XY: 46133 AN XY: 74304

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.645

Alfa AF: 0.570 Hom.: 1998

Bravo AF: 0.604

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	18
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7552384; hg19: chr1-64237404;