rs2246298

Variant names:

• chr9-104928452-G-A
• rs2246298
• ENST00000435915.1:n.359-330G>A

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,066 control chromosomes in the GnomAD database, including 2,894 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 0.18 (2894 hom., cov: 33)
• Consequence: ENSG00000226334 ENST00000435915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 4 publications found

Genes affected

ENSG00000226334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435915.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105376196	NR_188620.1		n.1122+542G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226334	ENST00000435915.1	TSL:3	n.359-330G>A		intron	N/A
	ENSG00000226334	ENST00000820514.1		n.1164+542G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26628 AN: 151946 Hom.: 2900 Cov.: 33

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.175 AC: 26627 AN: 152066 Hom.: 2894 Cov.: 33 AF XY: 0.180 AC XY: 13409 AN XY: 74318

African (AFR) AF: 0.0558 AC: 2319 AN: 41556

American (AMR) AF: 0.172 AC: 2636 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3464

East Asian (EAS) AF: 0.293 AC: 1507 AN: 5136

South Asian (SAS) AF: 0.339 AC: 1627 AN: 4798

European-Finnish (FIN) AF: 0.276 AC: 2911 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14065 AN: 67946

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.164 Hom.: 377

Bravo AF: 0.163

Asia WGS AF: 0.293 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.036
DANN	Benign	0.88
PhyloP100		-2.7
PromoterAI		-0.072	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2246298; hg19: chr9-107690733;