8-42694504-C-T

Position:

• chr8-42694504-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.673

Alfa AF: 0.642 Hom.: 5648

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1955185; hg19: chr8-42549647;