rs3934516

chr15-61311780-G-Cchr15-61311780-G-T

Variant summary

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

The ENST00000559783.2(ENSG00000259616):n.237-11241C>G 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 0.115 in 151,614 control chromosomes in the GnomAD database, including 1,749 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 (1749 hom., cov: 32)
• Consequence: ENST00000559783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

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 (AFR) allele frequency at 95% confidence interval = 0.268 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
	ENST00000559783.2	n.237-11241C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17350 AN: 151498 Hom.: 1733 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.115 AC: 17401 AN: 151614 Hom.: 1749 Cov.: 32 AF XY: 0.112 AC XY: 8276 AN XY: 74032

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0138

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0798 Hom.: 113

Bravo AF: 0.124

Asia WGS AF: 0.0550 AC: 191 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	0.092
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3934516; hg19: chr15-61603979;