rs972275

Variant names:

• chr6-127070699-C-G
• rs972275
• ENST00000652419.1:n.479G>C

Variant summary

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

The ENST00000652419.1(ENSG00000293110):​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: ENSG00000293110 ENST00000652419.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 16 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652419.1. 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
	ENSG00000293110	ENST00000652419.1		n.479G>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000293110	ENST00000718754.1		n.797G>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000293110	ENST00000650648.1		n.476+313G>C		intron	N/A

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

African (AFR) AF: 0.349 AC: 14464 AN: 41428

American (AMR) AF: 0.384 AC: 5838 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1635 AN: 3462

East Asian (EAS) AF: 0.548 AC: 2827 AN: 5160

South Asian (SAS) AF: 0.466 AC: 2244 AN: 4812

European-Finnish (FIN) AF: 0.377 AC: 3979 AN: 10546

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26127 AN: 67830

Other (OTH) AF: 0.418 AC: 880 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.30
DANN	Benign	0.35
PhyloP100		-0.80

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: rs972275;

hg19: chr6-127391844;

COSMIC: COSV69425951;