6-6742916-T-G

Variant names:

• chr6-6742916-T-G
• rs1294421
• ENST00000776241.1:n.579T>G

Variant summary

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

The ENST00000776241.1(ENSG00000287497):​n.579T>G 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 0.619 in 152,102 control chromosomes in the GnomAD database, including 30,059 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 0.62 (30059 hom., cov: 32)
• Consequence: ENSG00000287497 ENST00000776241.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 80 publications found

Genes affected

ENSG00000287497 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776241.1. 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
	LOC101928004	NR_187687.1		n.486-31058A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287497	ENST00000776241.1		n.579T>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000226281	ENST00000689004.1		n.563+2021A>C		intron	N/A
	ENSG00000226281	ENST00000775982.1		n.265-31058A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94113 AN: 151986 Hom.: 30030 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.619 AC: 94176 AN: 152102 Hom.: 30059 Cov.: 32 AF XY: 0.608 AC XY: 45236 AN XY: 74348

African (AFR) AF: 0.744 AC: 30884 AN: 41494

American (AMR) AF: 0.513 AC: 7837 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5174

South Asian (SAS) AF: 0.412 AC: 1988 AN: 4828

European-Finnish (FIN) AF: 0.599 AC: 6329 AN: 10566

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41943 AN: 67974

Other (OTH) AF: 0.581 AC: 1224 AN: 2106

Alfa AF: 0.608 Hom.: 76729

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.41
PhyloP100		-1.5

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: rs1294421;

hg19: chr6-6743149;