rs314590

Variant names:

• chr7-4434501-G-A
• rs314590
• ENST00000741164.1:n.153G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-4434501-G-A
• chr7-4434501-G-C

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.153G>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 0.899 in 152,316 control chromosomes in the GnomAD database, including 61,818 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 0.90 (61818 hom., cov: 34)
• Consequence: ENSG00000296681 ENST00000741164.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 5 publications found

Genes affected

ENSG00000296681 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.918 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741164.1. 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
	ENSG00000296681	ENST00000741164.1		n.153G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000296681	ENST00000741167.1		n.193G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296681	ENST00000741168.1		n.233G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136889 AN: 152198 Hom.: 61775 Cov.: 34

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.899 AC: 136986 AN: 152316 Hom.: 61818 Cov.: 34 AF XY: 0.894 AC XY: 66608 AN XY: 74472

African (AFR) AF: 0.926 AC: 38499 AN: 41576

American (AMR) AF: 0.826 AC: 12638 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3324 AN: 3472

East Asian (EAS) AF: 0.777 AC: 4023 AN: 5180

South Asian (SAS) AF: 0.831 AC: 4015 AN: 4830

European-Finnish (FIN) AF: 0.887 AC: 9420 AN: 10620

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.911 AC: 62007 AN: 68028

Other (OTH) AF: 0.914 AC: 1932 AN: 2114

Alfa AF: 0.902 Hom.: 52282

Bravo AF: 0.896

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.71
PhyloP100		-0.52

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: rs314590;

hg19: chr7-4474132;