chr4-141564956-A-G

Position:

• chr4-141564956-A-G

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 0.507 in 152,108 control chromosomes in the GnomAD database, including 19,682 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 0.51 (19682 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

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 (SAS) allele frequency at 95% confidence interval = 0.541 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: 0.507 AC: 77127 AN: 151990 Hom.: 19684 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.507 AC: 77150 AN: 152108 Hom.: 19682 Cov.: 33 AF XY: 0.508 AC XY: 37809 AN XY: 74378

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.487

Alfa AF: 0.537 Hom.: 11170

Bravo AF: 0.490

Asia WGS AF: 0.536 AC: 1863 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	4.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2322182; hg19: chr4-142486109;