chr15-61311780-G-C

Variant names:

• chr15-61311780-G-C
• rs3934516
• ENST00000559783.2:n.237-11241C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559783.2(ENSG00000259675):​n.237-11241C>G variant causes a intron 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: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 1 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559783.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259675	ENST00000559783.2	TSL:3	n.237-11241C>G		intron	N/A

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

African (AFR) AF: 0.273 AC: 11261 AN: 41304

American (AMR) AF: 0.0755 AC: 1151 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.0138 AC: 71 AN: 5142

South Asian (SAS) AF: 0.0552 AC: 264 AN: 4786

European-Finnish (FIN) AF: 0.0265 AC: 277 AN: 10438

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.0543 AC: 3692 AN: 67936

Other (OTH) AF: 0.105 AC: 221 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.092
DANN	Benign	0.60
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3934516; hg19: chr15-61603979;