rs12237914

Variant names:

• chr9-6306896-A-G
• rs12237914
• ENST00000722750.1:n.103-15855T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-6306896-A-G
• chr9-6306896-A-T

Variant summary

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

The ENST00000722750.1(ENSG00000294323):​n.103-15855T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,044 control chromosomes in the GnomAD database, including 9,739 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 0.34 (9739 hom., cov: 32)
• Consequence: ENSG00000294323 ENST00000722750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 6 publications found

Genes affected

ENSG00000294323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987046	XR_001746613.3	n.69-15855T>C		intron_variant	Intron 1 of 2
LOC107987046	XR_001746614.2	n.69-15855T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294323	ENST00000722750.1	n.103-15855T>C		intron_variant	Intron 1 of 3
ENSG00000294323	ENST00000722751.1	n.104-15855T>C		intron_variant	Intron 1 of 4
ENSG00000294323	ENST00000722752.1	n.223+3608T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51961 AN: 151926 Hom.: 9721 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.342 AC: 51972 AN: 152044 Hom.: 9739 Cov.: 32 AF XY: 0.341 AC XY: 25327 AN XY: 74330

African (AFR) AF: 0.202 AC: 8390 AN: 41480

American (AMR) AF: 0.302 AC: 4611 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2746 AN: 5156

South Asian (SAS) AF: 0.407 AC: 1965 AN: 4824

European-Finnish (FIN) AF: 0.390 AC: 4121 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27361 AN: 67952

Other (OTH) AF: 0.348 AC: 736 AN: 2114

Alfa AF: 0.382 Hom.: 22709

Bravo AF: 0.327

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.80
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12237914; hg19: chr9-6306896;