rs16909225

Variant names:

• chr8-81484124-A-G
• rs16909225
• ENST00000524085.2:n.299-13793A>G

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-13793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,246 control chromosomes in the GnomAD database, including 1,938 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 0.16 (1938 hom., cov: 33)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 3 publications found

Genes affected

ENSG00000253374 (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 (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+22150A>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-13793A>G		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-37583A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-37583A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-37583A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23832 AN: 152128 Hom.: 1925 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.157 AC: 23885 AN: 152246 Hom.: 1938 Cov.: 33 AF XY: 0.154 AC XY: 11494 AN XY: 74462

African (AFR) AF: 0.164 AC: 6814 AN: 41526

American (AMR) AF: 0.145 AC: 2217 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.0673 AC: 349 AN: 5188

South Asian (SAS) AF: 0.172 AC: 832 AN: 4826

European-Finnish (FIN) AF: 0.116 AC: 1235 AN: 10610

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11385 AN: 68006

Other (OTH) AF: 0.157 AC: 331 AN: 2114

Alfa AF: 0.164 Hom.: 721

Bravo AF: 0.157

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs16909225; hg19: chr8-82396359;