6-127070699-C-G

Position:

• chr6-127070699-C-G

Variant summary

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

The ENST00000652419.1(ENSG00000286215):​n.479G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,760 control chromosomes in the GnomAD database, including 11,405 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 (11405 hom., cov: 31)
• Consequence: ENSG00000286215 ENST00000652419.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

ENSG00000286215 (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 (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3400+313G>C		intron_variant
LOC105377989	XR_007059743.1	n.564+313G>C		intron_variant
LOC105377989	XR_007059744.1	n.564+313G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286215	ENST00000652419.1	n.479G>C		non_coding_transcript_exon_variant	2/2
ENSG00000286215	ENST00000650648.1	n.476+313G>C		intron_variant
ENSG00000286215	ENST00000650684.1	n.548+313G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58427 AN: 151642 Hom.: 11392 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.385 AC: 58456 AN: 151760 Hom.: 11405 Cov.: 31 AF XY: 0.389 AC XY: 28852 AN XY: 74154

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.418

Alfa AF: 0.394 Hom.: 6708

Bravo AF: 0.382

Asia WGS AF: 0.468 AC: 1625 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	0.30
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972275; hg19: chr6-127391844; COSMIC: COSV69425951;