chr4-141564956-A-G

Variant names:

• chr4-141564956-A-G
• rs2322182

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.449 AC: 18638 AN: 41470

American (AMR) AF: 0.418 AC: 6392 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1969 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2482 AN: 5178

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4830

European-Finnish (FIN) AF: 0.591 AC: 6250 AN: 10568

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36984 AN: 67990

Other (OTH) AF: 0.487 AC: 1029 AN: 2112

Alfa AF: 0.538 Hom.: 12323

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
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs2322182; hg19: chr4-142486109;