rs17542930

chr2-48859145-T-Cchr2-48859145-T-G

Variant summary

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

The ENST00000634588.1(ENSG00000282890):n.302+49504T>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 0.114 in 152,260 control chromosomes in the GnomAD database, including 1,237 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 0.11 (1237 hom., cov: 33)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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
	ENST00000634588.1	n.302+49504T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17353 AN: 152142 Hom.: 1238 Cov.: 33

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.114 AC: 17343 AN: 152260 Hom.: 1237 Cov.: 33 AF XY: 0.117 AC XY: 8721 AN XY: 74454

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.0954

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0806 Hom.: 144

Bravo AF: 0.105

Asia WGS AF: 0.132 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.11
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17542930; hg19: chr2-49086284;