chr15-95644576-C-T

Variant names:

• chr15-95644576-C-T
• rs17504636
• ENST00000611285.1:n.26+6057C>T

Variant summary

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

The ENST00000611285.1(ENSG00000275016):​n.26+6057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,916 control chromosomes in the GnomAD database, including 3,987 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 0.23 (3987 hom., cov: 32)
• Consequence: ENSG00000275016 ENST00000611285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 2 publications found

Genes affected

ENSG00000275016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 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
ENSG00000275016	ENST00000611285.1	n.26+6057C>T		intron_variant	Intron 1 of 1	5
ENSG00000275016	ENST00000612595.2	n.204+6057C>T		intron_variant	Intron 1 of 2	5
ENSG00000275016	ENST00000614344.6	n.201+6057C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34281 AN: 151798 Hom.: 3978 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.226 AC: 34316 AN: 151916 Hom.: 3987 Cov.: 32 AF XY: 0.225 AC XY: 16729 AN XY: 74236

African (AFR) AF: 0.238 AC: 9865 AN: 41396

American (AMR) AF: 0.253 AC: 3858 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 703 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5156

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4812

European-Finnish (FIN) AF: 0.217 AC: 2288 AN: 10558

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14411 AN: 67966

Other (OTH) AF: 0.240 AC: 507 AN: 2116

Alfa AF: 0.218 Hom.: 12323

Bravo AF: 0.231

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	6.1
DANN	Benign	0.59
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs17504636; hg19: chr15-96187805;