rs9302534

Variant names:

• chr16-17954853-T-C
• rs9302534
• ENST00000569048.5:n.405+12690A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-17954853-T-C
• chr16-17954853-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000824815.1(ENSG00000259929):​n.146+12690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,144 control chromosomes in the GnomAD database, including 19,696 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 0.48 (19696 hom., cov: 33)
• Consequence: ENSG00000259929 ENST00000824815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55
• Publications: 6 publications found

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824815.1. 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
	ENSG00000259929	ENST00000569048.5	TSL:5	n.405+12690A>G		intron	N/A
	ENSG00000259929	ENST00000824815.1		n.146+12690A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72635 AN: 152024 Hom.: 19656 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.478 AC: 72719 AN: 152144 Hom.: 19696 Cov.: 33 AF XY: 0.470 AC XY: 34991 AN XY: 74384

African (AFR) AF: 0.755 AC: 31342 AN: 41490

American (AMR) AF: 0.357 AC: 5459 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1050 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2237 AN: 5176

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4826

European-Finnish (FIN) AF: 0.363 AC: 3848 AN: 10586

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25741 AN: 67986

Other (OTH) AF: 0.425 AC: 899 AN: 2114

Alfa AF: 0.394 Hom.: 20814

Bravo AF: 0.492

Asia WGS AF: 0.399 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.63
PhyloP100		3.5

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: rs9302534;

hg19: chr16-18048710;