rs2422493

Variant names:

• chr9-104928714-G-A
• rs2422493
• ENST00000435915.1:n.359-68G>A

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-68G>A 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 151,904 control chromosomes in the GnomAD database, including 17,594 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 (17590 hom., cov: 31)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: ENSG00000226334 ENST00000435915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 52 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 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.1123-794G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226334	ENST00000435915.1	TSL:3	n.359-68G>A		intron	N/A
	ENSG00000226334	ENST00000820514.1		n.1164+804G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72587 AN: 151754 Hom.: 17584 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.500 AC: 16 AN: 32 Hom.: 4 AF XY: 0.464 AC XY: 13 AN XY: 28

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 14 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.478 AC: 72625 AN: 151872 Hom.: 17590 Cov.: 31 AF XY: 0.483 AC XY: 35868 AN XY: 74226

African (AFR) AF: 0.440 AC: 18222 AN: 41422

American (AMR) AF: 0.535 AC: 8157 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2262 AN: 5154

South Asian (SAS) AF: 0.530 AC: 2545 AN: 4798

European-Finnish (FIN) AF: 0.570 AC: 6010 AN: 10542

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31693 AN: 67918

Other (OTH) AF: 0.484 AC: 1023 AN: 2114

Alfa AF: 0.470 Hom.: 25993

Bravo AF: 0.474

Asia WGS AF: 0.479 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.52
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2422493; hg19: chr9-107690995;