4-147361190-T-C

Position:

• chr4-147361190-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 0.941 in 152,284 control chromosomes in the GnomAD database, including 67,453 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 0.94 (67453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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: 0.941 AC: 143164 AN: 152166 Hom.: 67429 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.941 AC: 143243 AN: 152284 Hom.: 67453 Cov.: 32 AF XY: 0.940 AC XY: 69958 AN XY: 74456

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.962

Gnomad4 OTH AF: 0.922

Alfa AF: 0.952 Hom.: 29466

Bravo AF: 0.937

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429138; hg19: chr4-148282342;