5-138283236-G-C

Position:

• chr5-138283236-G-C

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 0.309 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.138283236G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.330

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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