chr8-16042179-A-G

Variant names:

• chr8-16042179-A-G
• rs765262

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 0.25 in 152,014 control chromosomes in the GnomAD database, including 4,967 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 0.25 (4967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.250 AC: 37966 AN: 151896 Hom.: 4969 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.250 AC: 37978 AN: 152014 Hom.: 4967 Cov.: 32 AF XY: 0.246 AC XY: 18313 AN XY: 74294

African (AFR) AF: 0.199 AC: 8233 AN: 41458

American (AMR) AF: 0.214 AC: 3262 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3464

East Asian (EAS) AF: 0.103 AC: 533 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4814

European-Finnish (FIN) AF: 0.255 AC: 2702 AN: 10576

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19969 AN: 67948

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.273 Hom.: 24914

Bravo AF: 0.239

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.38
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs765262; hg19: chr8-15899688;