chr8-56257174-T-C

Variant names:

• chr8-56257174-T-C
• rs6474053

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 0.161 in 151,708 control chromosomes in the GnomAD database, including 2,005 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 0.16 (2005 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24477 AN: 151592 Hom.: 2002 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.161 AC: 24490 AN: 151708 Hom.: 2005 Cov.: 31 AF XY: 0.159 AC XY: 11819 AN XY: 74160

African (AFR) AF: 0.202 AC: 8371 AN: 41340

American (AMR) AF: 0.166 AC: 2535 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3458

East Asian (EAS) AF: 0.0619 AC: 320 AN: 5166

South Asian (SAS) AF: 0.140 AC: 673 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1469 AN: 10482

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9890 AN: 67884

Other (OTH) AF: 0.183 AC: 384 AN: 2102

Alfa AF: 0.0882 Hom.: 131

Bravo AF: 0.166

Asia WGS AF: 0.128 AC: 444 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6474053; hg19: chr8-57169733;