6-131440537-C-T

Position:

• chr6-131440537-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702750.1(ENSG00000290067):​n.188-313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,960 control chromosomes in the GnomAD database, including 18,272 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 0.42 (18272 hom., cov: 31)
• Consequence: ENSG00000290067 ENST00000702750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

ENSG00000290067 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378005	XR_001744344.2	n.181-313G>A		intron_variant
LOC105378005	XR_007059769.1	n.432-313G>A		intron_variant
LOC105378005	XR_007059770.1	n.432-297G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290067	ENST00000702750.1	n.188-313G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63513 AN: 151842 Hom.: 18217 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.419 AC: 63633 AN: 151960 Hom.: 18272 Cov.: 31 AF XY: 0.409 AC XY: 30376 AN XY: 74258

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.427

Alfa AF: 0.297 Hom.: 16969

Bravo AF: 0.451

Asia WGS AF: 0.202 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2078265; hg19: chr6-131761677;