rs16928254

Variant names:

• chr9-11952979-G-A
• rs16928254
• ENST00000649122.1:n.388+25040G>A

Variant summary

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

The ENST00000649122.1(ENSG00000285784):​n.388+25040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 151,636 control chromosomes in the GnomAD database, including 172 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 0.039 (172 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 1 publications found

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.083 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
ENSG00000285784	ENST00000649122.1	n.388+25040G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5940 AN: 151516 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0392 AC: 5937 AN: 151636 Hom.: 172 Cov.: 32 AF XY: 0.0384 AC XY: 2846 AN XY: 74128

African (AFR) AF: 0.0165 AC: 682 AN: 41334

American (AMR) AF: 0.0269 AC: 409 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0370 AC: 128 AN: 3458

East Asian (EAS) AF: 0.0898 AC: 462 AN: 5146

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4802

European-Finnish (FIN) AF: 0.0476 AC: 504 AN: 10594

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3572 AN: 67792

Other (OTH) AF: 0.0290 AC: 61 AN: 2104

Alfa AF: 0.0403 Hom.: 36

Bravo AF: 0.0373

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs16928254; hg19: chr9-11952979;