1-63771733-G-C

Variant names:

• chr1-63771733-G-C
• rs7552384

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 0.617 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.272 AC: 11280 AN: 41404

American (AMR) AF: 0.738 AC: 11281 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3468

East Asian (EAS) AF: 0.819 AC: 4224 AN: 5156

South Asian (SAS) AF: 0.633 AC: 3055 AN: 4824

European-Finnish (FIN) AF: 0.776 AC: 8203 AN: 10570

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50902 AN: 67958

Other (OTH) AF: 0.645 AC: 1360 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	18
DANN	Benign	0.75
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs7552384; hg19: chr1-64237404;