chr15-78394481-A-G

Variant names:

• chr15-78394481-A-G
• rs11635084
• ENST00000760515.1:n.229+3068A>G

Variant summary

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

The ENST00000760515.1(ENSG00000299108):​n.229+3068A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,962 control chromosomes in the GnomAD database, including 19,394 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 0.49 (19394 hom., cov: 31)
• Consequence: ENSG00000299108 ENST00000760515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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
ENSG00000299108	ENST00000760515.1	n.229+3068A>G		intron_variant	Intron 2 of 2
ENSG00000299108	ENST00000760516.1	n.237+3068A>G		intron_variant	Intron 2 of 4
ENSG00000299108	ENST00000760517.1	n.223-1640A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73636 AN: 151844 Hom.: 19362 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.485 AC: 73709 AN: 151962 Hom.: 19394 Cov.: 31 AF XY: 0.486 AC XY: 36122 AN XY: 74256

African (AFR) AF: 0.700 AC: 29000 AN: 41454

American (AMR) AF: 0.382 AC: 5834 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2800 AN: 5150

South Asian (SAS) AF: 0.391 AC: 1883 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4886 AN: 10542

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26492 AN: 67952

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.419 Hom.: 43883

Bravo AF: 0.493

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.58
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11635084; hg19: chr15-78686823;