6-127093656-C-T

Variant names:

• chr6-127093656-C-T
• rs719726
• ENST00000650841.1:n.3338G>A

Variant summary

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

The ENST00000650841.1(ENSG00000286215):​n.3338G>A 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 0.603 in 151,840 control chromosomes in the GnomAD database, including 27,821 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 0.60 (27821 hom., cov: 31)
• Consequence: ENSG00000286215 ENST00000650841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3326-22570G>A		intron_variant	Intron 4 of 13
LOC105377989	XR_007059743.1	n.490-22570G>A		intron_variant	Intron 3 of 8
LOC105377989	XR_007059744.1	n.490-22570G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286215	ENST00000650841.1	n.3338G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000286215	ENST00000650648.1	n.402-22570G>A		intron_variant	Intron 3 of 7
ENSG00000286215	ENST00000650684.1	n.474-22570G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91399 AN: 151722 Hom.: 27773 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.603 AC: 91499 AN: 151840 Hom.: 27821 Cov.: 31 AF XY: 0.598 AC XY: 44360 AN XY: 74184

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.578

Alfa AF: 0.588 Hom.: 11415

Bravo AF: 0.611

Asia WGS AF: 0.577 AC: 2004 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719726; hg19: chr6-127414801; COSMIC: COSV60280637;