chr1-247458850-C-T

Variant names:

• chr1-247458850-C-T
• rs72655377

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 0.151 in 151,986 control chromosomes in the GnomAD database, including 1,793 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 0.15 (1793 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.151 AC: 22888 AN: 151868 Hom.: 1796 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.151 AC: 22894 AN: 151986 Hom.: 1793 Cov.: 30 AF XY: 0.151 AC XY: 11227 AN XY: 74248

African (AFR) AF: 0.161 AC: 6656 AN: 41420

American (AMR) AF: 0.122 AC: 1862 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3472

East Asian (EAS) AF: 0.0596 AC: 308 AN: 5166

South Asian (SAS) AF: 0.0830 AC: 400 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2204 AN: 10560

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10274 AN: 67974

Other (OTH) AF: 0.140 AC: 294 AN: 2106

Alfa AF: 0.124 Hom.: 478

Bravo AF: 0.145

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.38
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs72655377; hg19: chr1-247622152;