chr4-156433098-T-C

Position:

• chr4-156433098-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 0.06 in 152,232 control chromosomes in the GnomAD database, including 377 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 0.060 (377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0833 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: 0.0601 AC: 9139 AN: 152112 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0600 AC: 9140 AN: 152232 Hom.: 377 Cov.: 32 AF XY: 0.0585 AC XY: 4356 AN XY: 74434

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.0900

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0381 Hom.: 30

Bravo AF: 0.0597

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
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: rs13141142; hg19: chr4-157354250;