8-142040310-T-C

Variant names:

• chr8-142040310-T-C
• rs4917300

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 0.565 in 152,056 control chromosomes in the GnomAD database, including 24,517 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 0.56 (24517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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: 0.565 AC: 85808 AN: 151938 Hom.: 24496 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.565 AC: 85877 AN: 152056 Hom.: 24517 Cov.: 32 AF XY: 0.563 AC XY: 41832 AN XY: 74330

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.556

Alfa AF: 0.534 Hom.: 48133

Bravo AF: 0.579

Asia WGS AF: 0.582 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917300; hg19: chr8-143121671;