chr8-74974062-C-T

Variant names:

• chr8-74974062-C-T
• rs2925155

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 0.207 in 152,020 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.207 AC: 31461 AN: 151904 Hom.: 4002 Cov.: 33

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.207 AC: 31472 AN: 152020 Hom.: 4004 Cov.: 33 AF XY: 0.209 AC XY: 15523 AN XY: 74288

African (AFR) AF: 0.0525 AC: 2178 AN: 41506

American (AMR) AF: 0.283 AC: 4329 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3468

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5168

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4812

European-Finnish (FIN) AF: 0.274 AC: 2893 AN: 10552

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17483 AN: 67932

Other (OTH) AF: 0.235 AC: 495 AN: 2106

Alfa AF: 0.253 Hom.: 8992

Bravo AF: 0.204

Asia WGS AF: 0.298 AC: 1036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.0090
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2925155; hg19: chr8-75886297;