rs4777845

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 65 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370982	XR_007064770.1	n.1161-39314T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000543286.5	n.545+11850T>C		intron_variant	Intron 2 of 3	2
ENSG00000257060	ENST00000553478.1	n.318+11850T>C		intron_variant	Intron 2 of 3	4
ENSG00000257060	ENST00000554105.6	n.422+11850T>C		intron_variant	Intron 2 of 5	4

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

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.00847

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0327 Hom.: 84

Bravo AF: 0.0266

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4777845; hg19: chr15-93877425;