chr9-104928557-C-G

Variant names:

• chr9-104928557-C-G
• rs2246293
• ENST00000435915.1:n.359-225C>G

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-225C>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 152,154 control chromosomes in the GnomAD database, including 17,651 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 (17651 hom., cov: 34)
• Consequence: ENSG00000226334 ENST00000435915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 17 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105376196	NR_188620.1		n.1122+647C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226334	ENST00000435915.1	TSL:3	n.359-225C>G		intron	N/A
	ENSG00000226334	ENST00000820514.1		n.1164+647C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72769 AN: 152036 Hom.: 17647 Cov.: 34

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.478 AC: 72804 AN: 152154 Hom.: 17651 Cov.: 34 AF XY: 0.483 AC XY: 35965 AN XY: 74386

African (AFR) AF: 0.439 AC: 18238 AN: 41522

American (AMR) AF: 0.536 AC: 8190 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2253 AN: 5152

South Asian (SAS) AF: 0.531 AC: 2567 AN: 4830

European-Finnish (FIN) AF: 0.569 AC: 6013 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31818 AN: 68004

Other (OTH) AF: 0.483 AC: 1020 AN: 2112

Alfa AF: 0.347 Hom.: 929

Bravo AF: 0.474

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.49
DANN	Benign	0.67
PhyloP100		-2.1
PromoterAI		0.078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2246293; hg19: chr9-107690838;