15-78384471-G-T

Variant names:

• chr15-78384471-G-T
• rs4243079
• ENST00000760515.1:n.77-6790G>T

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.77-6790G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00891 in 152,212 control chromosomes in the GnomAD database, including 10 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 0.0089 (10 hom., cov: 32)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 1 publications found

Genes affected

ENSG00000299108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00891 (1356/152212) while in subpopulation AMR AF = 0.0205 (313/15298). AF 95% confidence interval is 0.0186. There are 10 homozygotes in GnomAd4. There are 667 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 10 gene

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
ENSG00000299108	ENST00000760515.1	n.77-6790G>T		intron_variant	Intron 1 of 2
ENSG00000299108	ENST00000760516.1	n.85-6790G>T		intron_variant	Intron 1 of 4
ENSG00000299108	ENST00000760517.1	n.70-6790G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00891 AC: 1355 AN: 152094 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.00910

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

GnomAD4 genome AF: 0.00891 AC: 1356 AN: 152212 Hom.: 10 Cov.: 32 AF XY: 0.00897 AC XY: 667 AN XY: 74390

African (AFR) AF: 0.00255 AC: 106 AN: 41540

American (AMR) AF: 0.0205 AC: 313 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00830 AC: 40 AN: 4818

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10588

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 708 AN: 68012

Other (OTH) AF: 0.00900 AC: 19 AN: 2110

Alfa AF: 0.00357 Hom.: 2199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.086
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4243079; hg19: chr15-78676813;