rs2129626

Positions:

• chr9-17071164-A-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, non coding transcript 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: ENST00000430545.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000430545.4	n.393+22123A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000649821.1	n.179+18164A>C		intron_variant, non_coding_transcript_variant

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;