15-93334196-T-C

Variant names:

• chr15-93334196-T-C
• rs4777845
• ENST00000543286.5:n.545+11850T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000543286.5(ENSG00000257060):​n.545+11850T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 152,298 control chromosomes in the GnomAD database, including 65 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 0.025 (65 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000543286.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 7 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0249 (3793/152298) while in subpopulation AMR AF = 0.0324 (495/15296). AF 95% confidence interval is 0.0309. There are 65 homozygotes in GnomAd4. There are 1774 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543286.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257060	ENST00000543286.5	TSL:2	n.545+11850T>C		intron	N/A
	ENSG00000257060	ENST00000553478.1	TSL:4	n.318+11850T>C		intron	N/A
	ENSG00000257060	ENST00000554105.6	TSL:4	n.422+11850T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0249 AC: 3791 AN: 152180 Hom.: 65 Cov.: 32

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00847

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0249 AC: 3793 AN: 152298 Hom.: 65 Cov.: 32 AF XY: 0.0238 AC XY: 1774 AN XY: 74470

African (AFR) AF: 0.0135 AC: 560 AN: 41564

American (AMR) AF: 0.0324 AC: 495 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5180

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4830

European-Finnish (FIN) AF: 0.00847 AC: 90 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0320 AC: 2175 AN: 68014

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0302 Hom.: 142

Bravo AF: 0.0266

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs4777845; hg19: chr15-93877425;