rs6931711

Variant names:

• chr6-27177807-C-T
• rs6931711
• ENST00000776751.1:n.426G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000776751.1(ENSG00000301163):​n.426G>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 0.0656 in 152,298 control chromosomes in the GnomAD database, including 604 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 0.066 (604 hom., cov: 32)
• Consequence: ENSG00000301163 ENST00000776751.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 publications found

Genes affected

ENSG00000301163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301163	ENST00000776751.1		n.426G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9989 AN: 152180 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0656 AC: 9985 AN: 152298 Hom.: 604 Cov.: 32 AF XY: 0.0697 AC XY: 5192 AN XY: 74460

African (AFR) AF: 0.0139 AC: 579 AN: 41586

American (AMR) AF: 0.0393 AC: 601 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3472

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5182

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4834

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5878 AN: 68016

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0730 Hom.: 198

Bravo AF: 0.0510

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6931711;

hg19: chr6-27145586;