rs626214

Variant names:

• chr9-32532471-A-C
• rs626214
• ENST00000681750.1:c.-45+18303T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-32532471-A-C
• chr9-32532471-A-T

Variant summary

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

The ENST00000681750.1(ENSG00000288684):​c.-45+18303T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,978 control chromosomes in the GnomAD database, including 20,358 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 0.51 (20358 hom., cov: 32)
• Consequence: ENSG00000288684 ENST00000681750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 11 publications found

Genes affected

ENSG00000288684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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
ENSG00000288684	ENST00000681750.1	c.-45+18303T>G		intron_variant	Intron 3 of 19			ENSP00000506413.1
ENSG00000288684	ENST00000680198.1	n.198+18303T>G		intron_variant	Intron 2 of 18			ENSP00000505143.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77624 AN: 151860 Hom.: 20334 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.511 AC: 77685 AN: 151978 Hom.: 20358 Cov.: 32 AF XY: 0.507 AC XY: 37634 AN XY: 74290

African (AFR) AF: 0.629 AC: 26045 AN: 41424

American (AMR) AF: 0.440 AC: 6715 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2057 AN: 5172

South Asian (SAS) AF: 0.567 AC: 2726 AN: 4806

European-Finnish (FIN) AF: 0.380 AC: 4017 AN: 10568

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33074 AN: 67950

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.493 Hom.: 75725

Bravo AF: 0.515

Asia WGS AF: 0.450 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs626214; hg19: chr9-32532469;