rs2024134

Positions:

• chr17-11210815-T-G

Variant summary

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

The ENST00000648331.1(ENSG00000285541):​n.99-11125A>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 0.682 in 151,518 control chromosomes in the GnomAD database, including 39,007 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 (39007 hom., cov: 29)
• Consequence: ENST00000648331.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 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
	ENST00000648331.1	n.99-11125A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103283 AN: 151400 Hom.: 39011 Cov.: 29

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.682 AC: 103289 AN: 151518 Hom.: 39007 Cov.: 29 AF XY: 0.684 AC XY: 50618 AN XY: 73984

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.686

Alfa AF: 0.809 Hom.: 80784

Bravo AF: 0.654

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024134; hg19: chr17-11114132;