15-98107885-G-T

Variant names:

• chr15-98107885-G-T
• rs11856483
• ENST00000560360.2:n.314-61146C>A

Variant summary

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

The ENST00000717124.1(ENSG00000259199):​n.292-61146C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,122 control chromosomes in the GnomAD database, including 886 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 0.091 (886 hom., cov: 32)
• Consequence: ENSG00000259199 ENST00000717124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88
• Publications: 0 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717124.1. 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
	ENSG00000259199	ENST00000560360.2	TSL:5	n.314-61146C>A		intron	N/A
	ENSG00000259199	ENST00000717124.1		n.292-61146C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13856 AN: 152004 Hom.: 887 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0910 AC: 13843 AN: 152122 Hom.: 886 Cov.: 32 AF XY: 0.0932 AC XY: 6928 AN XY: 74346

African (AFR) AF: 0.0206 AC: 857 AN: 41524

American (AMR) AF: 0.0649 AC: 992 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5164

South Asian (SAS) AF: 0.0986 AC: 474 AN: 4808

European-Finnish (FIN) AF: 0.163 AC: 1727 AN: 10568

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7979 AN: 67994

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0812 Hom.: 304

Bravo AF: 0.0808

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.38
PhyloP100		-3.9

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: rs11856483; hg19: chr15-98651114;