5-140347056-C-T

Variant names:

• chr5-140347056-C-T
• rs4150196

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 0.527 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
• Publications: 17 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.641 AC: 26612 AN: 41490

American (AMR) AF: 0.499 AC: 7629 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2246 AN: 5174

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4818

European-Finnish (FIN) AF: 0.566 AC: 5987 AN: 10572

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31932 AN: 67956

Other (OTH) AF: 0.500 AC: 1057 AN: 2112

Alfa AF: 0.486 Hom.: 24062

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
PhyloP100		0.19
PromoterAI		0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4150196; hg19: chr5-139726641;