rs11635160

chr15-84148033-G-A

Variant summary

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

The ENST00000558550.2(ENSG00000291062):n.1141-16366G>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 0.172 in 152,130 control chromosomes in the GnomAD database, including 2,507 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 0.17 (2507 hom., cov: 30)
• Consequence: ENST00000558550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558550.2	n.1141-16366G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000701714.1	n.1301-16366G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26186 AN: 152012 Hom.: 2509 Cov.: 30

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.172 AC: 26184 AN: 152130 Hom.: 2507 Cov.: 30 AF XY: 0.171 AC XY: 12693 AN XY: 74376

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.204

Alfa AF: 0.187 Hom.: 352

Bravo AF: 0.166

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.026
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11635160; hg19: chr15-84816785;