chr4-156042540-G-A

Position:

• chr4-156042540-G-A

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 0.306 in 151,254 control chromosomes in the GnomAD database, including 8,969 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 0.31 (8969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.306 AC: 46293 AN: 151138 Hom.: 8967 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.306 AC: 46303 AN: 151254 Hom.: 8969 Cov.: 32 AF XY: 0.299 AC XY: 22085 AN XY: 73806

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.313

Alfa AF: 0.398 Hom.: 15919

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 869 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4691238; hg19: chr4-156963692;