8-74974062-C-T

Position:

• chr8-74974062-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 0.207 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.207 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

Gnomad4 AFR AF: 0.0525

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.235

Alfa AF: 0.254 Hom.: 6971

Bravo AF: 0.204

Asia WGS AF: 0.298 AC: 1036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925155; hg19: chr8-75886297;