8-42694504-C-T

Variant names:

• chr8-42694504-C-T
• rs1955185

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 0.639 in 151,968 control chromosomes in the GnomAD database, including 34,302 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 0.64 (34302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97070 AN: 151848 Hom.: 34292 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.639 AC: 97106 AN: 151968 Hom.: 34302 Cov.: 31 AF XY: 0.644 AC XY: 47805 AN XY: 74260

African (AFR) AF: 0.312 AC: 12903 AN: 41416

American (AMR) AF: 0.714 AC: 10890 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2448 AN: 3466

East Asian (EAS) AF: 0.807 AC: 4165 AN: 5164

South Asian (SAS) AF: 0.712 AC: 3427 AN: 4816

European-Finnish (FIN) AF: 0.760 AC: 8026 AN: 10560

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52876 AN: 67970

Other (OTH) AF: 0.673 AC: 1420 AN: 2110

Alfa AF: 0.633 Hom.: 5697

Bravo AF: 0.620

Asia WGS AF: 0.710 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1955185; hg19: chr8-42549647;