rs4150196

chr5-140347056-C-T

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 0.527 in 152,072 control chromosomes in the GnomAD database, including 21,758 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 0.53 (21758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.527 AC: 80065 AN: 151952 Hom.: 21708 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.527 AC: 80183 AN: 152072 Hom.: 21758 Cov.: 32 AF XY: 0.530 AC XY: 39414 AN XY: 74344

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.500

Alfa AF: 0.482 Hom.: 11406

Bravo AF: 0.524

Asia WGS AF: 0.526 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4150196; hg19: chr5-139726641;