rs3935962

Variant names:

• chr15-61532102-A-C
• rs3935962
• ENST00000559783.2:n.124-24862T>G

Your query was ambiguous. Multiple possible variants found:

• chr15-61532102-A-C
• chr15-61532102-A-G
• chr15-61532102-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000559783.2(ENSG00000259675):​n.124-24862T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,874 control chromosomes in the GnomAD database, including 29,643 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 0.62 (29643 hom., cov: 31)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 3 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259675	ENST00000559783.2	TSL:3	n.124-24862T>G		intron	N/A
	ENSG00000259675	ENST00000748013.1		n.347-24862T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94794 AN: 151756 Hom.: 29616 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.625 AC: 94874 AN: 151874 Hom.: 29643 Cov.: 31 AF XY: 0.624 AC XY: 46335 AN XY: 74216

African (AFR) AF: 0.636 AC: 26313 AN: 41378

American (AMR) AF: 0.645 AC: 9860 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2121 AN: 3466

East Asian (EAS) AF: 0.758 AC: 3912 AN: 5164

South Asian (SAS) AF: 0.630 AC: 3033 AN: 4812

European-Finnish (FIN) AF: 0.630 AC: 6637 AN: 10536

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40882 AN: 67922

Other (OTH) AF: 0.607 AC: 1281 AN: 2112

Alfa AF: 0.609 Hom.: 14476

Bravo AF: 0.631

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.80
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3935962;

hg19: chr15-61824301;