6-137124222-C-T

Position:

• chr6-137124222-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 0.387 in 151,846 control chromosomes in the GnomAD database, including 11,697 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 0.39 (11697 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.137124222C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58783 AN: 151730 Hom.: 11691 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.387 AC: 58794 AN: 151846 Hom.: 11697 Cov.: 31 AF XY: 0.383 AC XY: 28392 AN XY: 74206

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.373

Alfa AF: 0.388 Hom.: 2167

Bravo AF: 0.394

Asia WGS AF: 0.301 AC: 1045 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321588; hg19: chr6-137445359;