15-95681992-G-T

Variant names:

• chr15-95681992-G-T
• rs4247092
• ENST00000611285.1:n.27-34401G>T

Variant summary

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

The ENST00000656202.1(ENSG00000275016):​n.155+29036G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,924 control chromosomes in the GnomAD database, including 10,316 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 0.34 (10316 hom., cov: 32)
• Consequence: ENSG00000275016 ENST00000656202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 4 publications found

Genes affected

ENSG00000275016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656202.1. 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
	ENSG00000275016	ENST00000611285.1	TSL:5	n.27-34401G>T		intron	N/A
	ENSG00000275016	ENST00000612595.2	TSL:5	n.204+43473G>T		intron	N/A
	ENSG00000275016	ENST00000614344.6	TSL:5	n.201+43473G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51800 AN: 151804 Hom.: 10321 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.341 AC: 51808 AN: 151924 Hom.: 10316 Cov.: 32 AF XY: 0.337 AC XY: 25015 AN XY: 74242

African (AFR) AF: 0.141 AC: 5843 AN: 41422

American (AMR) AF: 0.338 AC: 5158 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1209 AN: 5154

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4475 AN: 10516

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30987 AN: 67958

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.415 Hom.: 58558

Bravo AF: 0.325

Asia WGS AF: 0.237 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	8.7
DANN	Benign	0.56
PhyloP100		1.7

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: rs4247092;

hg19: chr15-96225221;