rs9298693

Variant names:

• chr9-13901410-G-A
• rs9298693
• ENST00000741129.1:n.1000-19420C>T

Variant summary

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

The ENST00000741129.1(ENSG00000289185):​n.1000-19420C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,626 control chromosomes in the GnomAD database, including 18,453 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 0.47 (18453 hom., cov: 30)
• Consequence: ENSG00000289185 ENST00000741129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 2 publications found

Genes affected

ENSG00000289185 (HGNC:58956):

LOC101929507 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741129.1. 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
	ENSG00000289185	ENST00000741129.1		n.1000-19420C>T		intron	N/A
	ENSG00000289185	ENST00000741130.1		n.1390+16686C>T		intron	N/A
	ENSG00000289185	ENST00000741131.1		n.932-19420C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71276 AN: 151508 Hom.: 18417 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.471 AC: 71373 AN: 151626 Hom.: 18453 Cov.: 30 AF XY: 0.458 AC XY: 33959 AN XY: 74116

African (AFR) AF: 0.666 AC: 27548 AN: 41336

American (AMR) AF: 0.375 AC: 5699 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3466

East Asian (EAS) AF: 0.104 AC: 532 AN: 5130

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4816

European-Finnish (FIN) AF: 0.319 AC: 3374 AN: 10562

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29141 AN: 67830

Other (OTH) AF: 0.494 AC: 1039 AN: 2104

Alfa AF: 0.458 Hom.: 2102

Bravo AF: 0.480

Asia WGS AF: 0.265 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		0.10

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: rs9298693;

hg19: chr9-13901409;

COSMIC: COSV60333996;