chr5-140138279-G-C

Variant names:

• chr5-140138279-G-C
• rs156093

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 0.375 in 151,990 control chromosomes in the GnomAD database, including 11,023 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 0.38 (11023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 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: 0.375 AC: 56997 AN: 151872 Hom.: 11015 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.375 AC: 57045 AN: 151990 Hom.: 11023 Cov.: 32 AF XY: 0.382 AC XY: 28378 AN XY: 74294

African (AFR) AF: 0.339 AC: 14025 AN: 41424

American (AMR) AF: 0.420 AC: 6411 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3203 AN: 5168

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3882 AN: 10560

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23941 AN: 67960

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.218 Hom.: 476

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.47
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs156093; hg19: chr5-139517864;