rs2129626

Variant names:

• chr9-17071164-A-C
• rs2129626
• ENST00000430545.4:n.393+22123A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430545.4(ENSG00000237153):​n.393+22123A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,248 control chromosomes in the GnomAD database, including 3,669 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 0.20 (3669 hom., cov: 33)
• Consequence: ENSG00000237153 ENST00000430545.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237153	ENST00000430545.4	n.393+22123A>C		intron_variant	Intron 2 of 2	5
ENSG00000237153	ENST00000649821.1	n.179+18164A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29957 AN: 152130 Hom.: 3670 Cov.: 33

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.197 AC: 29968 AN: 152248 Hom.: 3669 Cov.: 33 AF XY: 0.191 AC XY: 14187 AN XY: 74442

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.203

Alfa AF: 0.267 Hom.: 11630

Bravo AF: 0.189

Asia WGS AF: 0.208 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2129626; hg19: chr9-17071162;