6-131807424-C-T

Position:

• chr6-131807424-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 0.179 in 152,160 control chromosomes in the GnomAD database, including 3,169 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 0.18 (3169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

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 (AMR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27240 AN: 152042 Hom.: 3166 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.179 AC: 27250 AN: 152160 Hom.: 3169 Cov.: 32 AF XY: 0.175 AC XY: 13038 AN XY: 74386

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.171

Alfa AF: 0.233 Hom.: 6041

Bravo AF: 0.185

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800949; hg19: chr6-132128564;