rs1392635

Variant names:

• chr15-69105686-G-A
• rs1392635
• ENST00000822156.1:n.424+17903C>T

Variant summary

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

The ENST00000822156.1(ENSG00000306951):​n.424+17903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,074 control chromosomes in the GnomAD database, including 6,295 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 0.28 (6295 hom., cov: 32)
• Consequence: ENSG00000306951 ENST00000822156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 5 publications found

Genes affected

ENSG00000306951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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
ENSG00000306951	ENST00000822156.1	n.424+17903C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42618 AN: 151956 Hom.: 6277 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.281 AC: 42690 AN: 152074 Hom.: 6295 Cov.: 32 AF XY: 0.278 AC XY: 20664 AN XY: 74346

African (AFR) AF: 0.378 AC: 15680 AN: 41436

American (AMR) AF: 0.222 AC: 3389 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 953 AN: 3472

East Asian (EAS) AF: 0.166 AC: 858 AN: 5184

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4810

European-Finnish (FIN) AF: 0.224 AC: 2369 AN: 10564

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17217 AN: 68008

Other (OTH) AF: 0.255 AC: 537 AN: 2110

Alfa AF: 0.261 Hom.: 16760

Bravo AF: 0.280

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.44
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1392635; hg19: chr15-69398026;