rs1332408

Variant names:

• chr9-122429880-C-A
• rs1332408
• ENST00000431442.3:n.323+12995C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-122429880-C-A
• chr9-122429880-C-T

Variant summary

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

The ENST00000431442.3(ENSG00000234156):​n.323+12995C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,004 control chromosomes in the GnomAD database, including 4,648 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 0.25 (4648 hom., cov: 32)
• Consequence: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 4 publications found

Genes affected

ENSG00000234156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431442.3. 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
	ENSG00000234156	ENST00000431442.3	TSL:3	n.323+12995C>A		intron	N/A
	ENSG00000234156	ENST00000433572.3	TSL:3	n.357+12995C>A		intron	N/A
	ENSG00000234156	ENST00000723589.1		n.419+12995C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37443 AN: 151886 Hom.: 4643 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.247 AC: 37475 AN: 152004 Hom.: 4648 Cov.: 32 AF XY: 0.249 AC XY: 18497 AN XY: 74286

African (AFR) AF: 0.252 AC: 10444 AN: 41464

American (AMR) AF: 0.291 AC: 4443 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5168

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2151 AN: 10522

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15820 AN: 67966

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.238 Hom.: 14794

Bravo AF: 0.249

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1332408; hg19: chr9-125192159;