4-117962559-T-C

Position:

• chr4-117962559-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.68 (33463 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 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: 0.678 AC: 98067 AN: 144682 Hom.: 33442 Cov.: 20

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.678 AC: 98126 AN: 144756 Hom.: 33463 Cov.: 20 AF XY: 0.684 AC XY: 47870 AN XY: 69946

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.675

Alfa AF: 0.591 Hom.: 1621

Bravo AF: 0.725

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13138932; hg19: chr4-118883714;