7-2875744-G-T

Variant names:

• chr7-2875744-G-T
• rs6977940
• ENST00000715278.1:n.565G>T

Variant summary

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

The ENST00000715278.1(ENSG00000293592):​n.565G>T 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 0.144 in 152,232 control chromosomes in the GnomAD database, including 1,681 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 0.14 (1681 hom., cov: 33)
• Consequence: ENSG00000293592 ENST00000715278.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 6 publications found

Genes affected

ENSG00000293592 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715278.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293592	ENST00000715278.1		n.565G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000293592	ENST00000715279.1		n.458G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21954 AN: 152114 Hom.: 1679 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.144 AC: 21981 AN: 152232 Hom.: 1681 Cov.: 33 AF XY: 0.142 AC XY: 10584 AN XY: 74410

African (AFR) AF: 0.144 AC: 5991 AN: 41550

American (AMR) AF: 0.180 AC: 2749 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.149 AC: 718 AN: 4832

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10283 AN: 68010

Other (OTH) AF: 0.142 AC: 301 AN: 2116

Alfa AF: 0.144 Hom.: 3911

Bravo AF: 0.148

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.094
DANN	Benign	0.51
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6977940; hg19: chr7-2915378;