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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901579	XR_007060198.1	n.24G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296681	ENST00000741164.1	n.153G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000296681	ENST00000741167.1	n.193G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000296681	ENST00000741168.1	n.233G>A		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs314590; hg19: chr7-4474132;