rs265010

Variant names:

• chr5-79841354-G-A
• rs265010
• ENST00000665156.1:n.558G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-79841354-G-A
• chr5-79841354-G-C

Variant summary

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

The ENST00000665156.1(ENSG00000286818):​n.558G>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 0.734 in 152,132 control chromosomes in the GnomAD database, including 41,257 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 0.73 (41257 hom., cov: 32)
• Consequence: ENSG00000286818 ENST00000665156.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 1 publications found

Genes affected

ENSG00000286818 (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 = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665156.1. 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
	ENSG00000286818	ENST00000665156.1		n.558G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000286818	ENST00000827627.1		n.371G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286818	ENST00000827632.1		n.475G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111559 AN: 152014 Hom.: 41215 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.734 AC: 111655 AN: 152132 Hom.: 41257 Cov.: 32 AF XY: 0.734 AC XY: 54558 AN XY: 74352

African (AFR) AF: 0.818 AC: 33944 AN: 41516

American (AMR) AF: 0.708 AC: 10815 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3051 AN: 5178

South Asian (SAS) AF: 0.714 AC: 3436 AN: 4812

European-Finnish (FIN) AF: 0.720 AC: 7598 AN: 10560

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48351 AN: 67996

Other (OTH) AF: 0.718 AC: 1517 AN: 2112

Alfa AF: 0.723 Hom.: 9596

Bravo AF: 0.735

Asia WGS AF: 0.628 AC: 2186 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	0.48
DANN	Benign	0.11
PhyloP100		0.027

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: rs265010;

hg19: chr5-79137177;

COSMIC: COSV60158112;