15-94873085-C-T

Variant names:

• chr15-94873085-C-T
• rs11639294
• ENST00000614581.1:n.16+16222C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000618611.4(ENSG00000277654):​n.193+31834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,180 control chromosomes in the GnomAD database, including 2,288 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 0.16 (2288 hom., cov: 32)
• Consequence: ENSG00000277654 ENST00000618611.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

ENSG00000277654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 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
ENSG00000277654	ENST00000614581.1	n.16+16222C>T		intron_variant	Intron 1 of 4	5
ENSG00000277654	ENST00000615751.4	n.74+16222C>T		intron_variant	Intron 1 of 4	5
ENSG00000277654	ENST00000618377.1	n.330+16222C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24312 AN: 152062 Hom.: 2289 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.160 AC: 24325 AN: 152180 Hom.: 2288 Cov.: 32 AF XY: 0.161 AC XY: 11993 AN XY: 74414

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.171

Alfa AF: 0.172 Hom.: 869

Bravo AF: 0.153

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11639294; hg19: chr15-95416314;