rs2209875

Variant names:

• chr9-89198546-G-A
• rs2209875
• ENST00000842493.1:n.351-16780C>T

Variant summary

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

The ENST00000842493.1(ENSG00000309620):​n.351-16780C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,904 control chromosomes in the GnomAD database, including 6,797 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 0.29 (6797 hom., cov: 32)
• Consequence: ENSG00000309620 ENST00000842493.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 2 publications found

Genes affected

ENSG00000309620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842493.1. 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
	ENSG00000309620	ENST00000842493.1		n.351-16780C>T		intron	N/A
	ENSG00000309620	ENST00000842494.1		n.299-16796C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43471 AN: 151786 Hom.: 6770 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.287 AC: 43544 AN: 151904 Hom.: 6797 Cov.: 32 AF XY: 0.293 AC XY: 21748 AN XY: 74240

African (AFR) AF: 0.323 AC: 13365 AN: 41386

American (AMR) AF: 0.430 AC: 6568 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2447 AN: 5164

South Asian (SAS) AF: 0.270 AC: 1305 AN: 4832

European-Finnish (FIN) AF: 0.288 AC: 3044 AN: 10552

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15297 AN: 67928

Other (OTH) AF: 0.272 AC: 572 AN: 2106

Alfa AF: 0.267 Hom.: 719

Bravo AF: 0.302

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.14
PhyloP100		-0.91

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: rs2209875;

hg19: chr9-91813461;

COSMIC: COSV60374943;