rs11070188

Positions:

• chr15-39335142-A-G

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.67+85767T>C 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 0.754 in 152,076 control chromosomes in the GnomAD database, including 44,478 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 0.75 (44478 hom., cov: 31)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+85402T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.67+85767T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+24647T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000559318.1	n.409-35660T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114550 AN: 151958 Hom.: 44447 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.754 AC: 114626 AN: 152076 Hom.: 44478 Cov.: 31 AF XY: 0.751 AC XY: 55804 AN XY: 74308

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.776

Alfa AF: 0.799 Hom.: 12615

Bravo AF: 0.733

Asia WGS AF: 0.740 AC: 2575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11070188; hg19: chr15-39627343;