rs17786744

Variant names:

• chr8-23919493-A-G
• rs17786744
• ENST00000802606.1:n.92-628A>G

Variant summary

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

The ENST00000802606.1(ENSG00000304342):​n.92-628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,786 control chromosomes in the GnomAD database, including 10,731 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 0.37 (10731 hom., cov: 31)
• Consequence: ENSG00000304342 ENST00000802606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 39 publications found

Genes affected

ENSG00000304342 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802606.1. 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
	ENSG00000304342	ENST00000802606.1		n.92-628A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56169 AN: 151668 Hom.: 10729 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.370 AC: 56186 AN: 151786 Hom.: 10731 Cov.: 31 AF XY: 0.367 AC XY: 27246 AN XY: 74144

African (AFR) AF: 0.321 AC: 13314 AN: 41416

American (AMR) AF: 0.339 AC: 5157 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1788 AN: 5136

South Asian (SAS) AF: 0.135 AC: 648 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4728 AN: 10536

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

European-Non Finnish (NFE) AF: 0.415 AC: 28196 AN: 67882

Other (OTH) AF: 0.367 AC: 773 AN: 2104

Alfa AF: 0.396 Hom.: 19462

Bravo AF: 0.365

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.60
DANN	Benign	0.26
PhyloP100		0.041

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17786744;

hg19: chr8-23777006;