15-77559193-G-A

Variant names:

• chr15-77559193-G-A
• rs2137111
• ENST00000725805.1:n.213-9842G>A

Variant summary

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

The ENST00000725805.1(ENSG00000259420):​n.213-9842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,978 control chromosomes in the GnomAD database, including 3,352 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 0.20 (3352 hom., cov: 32)
• Consequence: ENSG00000259420 ENST00000725805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 12 publications found

Genes affected

ENSG00000259420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259420	ENST00000725805.1	n.213-9842G>A		intron_variant	Intron 2 of 4
ENSG00000259420	ENST00000725806.1	n.207-9842G>A		intron_variant	Intron 2 of 4
ENSG00000259420	ENST00000725808.1	n.115-9842G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30405 AN: 151858 Hom.: 3353 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.200 AC: 30403 AN: 151978 Hom.: 3352 Cov.: 32 AF XY: 0.202 AC XY: 14986 AN XY: 74298

African (AFR) AF: 0.107 AC: 4440 AN: 41440

American (AMR) AF: 0.249 AC: 3803 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1159 AN: 5168

South Asian (SAS) AF: 0.163 AC: 786 AN: 4816

European-Finnish (FIN) AF: 0.256 AC: 2704 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16031 AN: 67920

Other (OTH) AF: 0.200 AC: 420 AN: 2104

Alfa AF: 0.225 Hom.: 11717

Bravo AF: 0.197

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.90
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2137111; hg19: chr15-77851535;