rs265010

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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: ENST00000665156.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724557	XR_001742517.2	n.343G>A		non_coding_transcript_exon_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665156.1	n.558G>A		non_coding_transcript_exon_variant	1/3

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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.718

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs265010; hg19: chr5-79137177; COSMIC: COSV60158112;