rs17769090

Variant names:

• chr15-70337781-G-A
• rs17769090
• ENST00000819859.1:n.630+10077C>T

Variant summary

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

The ENST00000819859.1(ENSG00000306630):​n.630+10077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,040 control chromosomes in the GnomAD database, including 8,895 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 0.34 (8895 hom., cov: 32)
• Consequence: ENSG00000306630 ENST00000819859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 3 publications found

Genes affected

ENSG00000306630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819859.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306630	ENST00000819859.1		n.630+10077C>T		intron	N/A
	ENSG00000306630	ENST00000819860.1		n.172+10077C>T		intron	N/A
	ENSG00000306630	ENST00000819861.1		n.414+10077C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50991 AN: 151924 Hom.: 8898 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.335 AC: 51002 AN: 152040 Hom.: 8895 Cov.: 32 AF XY: 0.331 AC XY: 24613 AN XY: 74316

African (AFR) AF: 0.256 AC: 10609 AN: 41454

American (AMR) AF: 0.352 AC: 5379 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3472

East Asian (EAS) AF: 0.145 AC: 751 AN: 5186

South Asian (SAS) AF: 0.286 AC: 1378 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3899 AN: 10550

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26557 AN: 67948

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.370 Hom.: 32383

Bravo AF: 0.331

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.64
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs17769090; hg19: chr15-70630120;