rs4324715

Variant names:

• chr5-142289942-C-T
• rs4324715

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 0.409 in 151,834 control chromosomes in the GnomAD database, including 13,695 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 0.41 (13695 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 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: 0.409 AC: 62039 AN: 151716 Hom.: 13690 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.409 AC: 62054 AN: 151834 Hom.: 13695 Cov.: 31 AF XY: 0.410 AC XY: 30440 AN XY: 74168

African (AFR) AF: 0.236 AC: 9757 AN: 41388

American (AMR) AF: 0.518 AC: 7908 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2041 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1475 AN: 5146

South Asian (SAS) AF: 0.468 AC: 2243 AN: 4790

European-Finnish (FIN) AF: 0.409 AC: 4300 AN: 10512

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32802 AN: 67968

Other (OTH) AF: 0.455 AC: 959 AN: 2108

Alfa AF: 0.470 Hom.: 9304

Bravo AF: 0.406

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4324715; hg19: chr5-141669507;