chr5-138283236-G-C

Variant names:

• chr5-138283236-G-C
• rs6874130

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 0.309 in 151,944 control chromosomes in the GnomAD database, including 8,126 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 0.31 (8126 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46940 AN: 151826 Hom.: 8116 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.309 AC: 46971 AN: 151944 Hom.: 8126 Cov.: 31 AF XY: 0.313 AC XY: 23231 AN XY: 74292

African (AFR) AF: 0.422 AC: 17481 AN: 41398

American (AMR) AF: 0.312 AC: 4758 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3131 AN: 5164

South Asian (SAS) AF: 0.205 AC: 988 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2749 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15516 AN: 67972

Other (OTH) AF: 0.330 AC: 699 AN: 2116

Alfa AF: 0.280 Hom.: 807

Bravo AF: 0.327

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs6874130; hg19: chr5-137618925; COSMIC: COSV60398722;