4-117171981-T-C

Position:

• chr4-117171981-T-C

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 0.349 in 151,952 control chromosomes in the GnomAD database, including 9,421 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 0.35 (9421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53069 AN: 151834 Hom.: 9427 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.349 AC: 53067 AN: 151952 Hom.: 9421 Cov.: 32 AF XY: 0.355 AC XY: 26366 AN XY: 74264

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.337

Alfa AF: 0.352 Hom.: 13364

Bravo AF: 0.344

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10433903; hg19: chr4-118093137;