chr8-13774507-A-G

Variant names:

• chr8-13774507-A-G
• rs17254431

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 0.117 in 150,670 control chromosomes in the GnomAD database, including 1,413 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 0.12 (1413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• 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 (AMR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17686 AN: 150554 Hom.: 1413 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.117 AC: 17687 AN: 150670 Hom.: 1413 Cov.: 32 AF XY: 0.118 AC XY: 8722 AN XY: 73668

African (AFR) AF: 0.0616 AC: 2478 AN: 40208

American (AMR) AF: 0.173 AC: 2630 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3472

East Asian (EAS) AF: 0.0811 AC: 418 AN: 5152

South Asian (SAS) AF: 0.143 AC: 691 AN: 4818

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10544

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9245 AN: 67980

Other (OTH) AF: 0.140 AC: 294 AN: 2104

Alfa AF: 0.0601 Hom.: 88

Bravo AF: 0.119

Asia WGS AF: 0.110 AC: 382 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	4.4
DANN	Benign	0.77
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs17254431; hg19: chr8-13632016;