rs1471169

Positions:

• chr15-95119290-G-A
• chr15-95119290-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615751.4(ENSG00000293024):​n.435-3635G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,926 control chromosomes in the GnomAD database, including 34,887 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 0.68 (34887 hom., cov: 32)
• Consequence: ENST00000615751.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370991	XR_002957693.2	n.488-3635G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615751.4	n.435-3635G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000658436.1	n.187-27020C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102618 AN: 151806 Hom.: 34857 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.676 AC: 102696 AN: 151926 Hom.: 34887 Cov.: 32 AF XY: 0.675 AC XY: 50087 AN XY: 74246

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.688

Alfa AF: 0.704 Hom.: 76298

Bravo AF: 0.674

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1471169; hg19: chr15-95662519;