rs12538332

Variant names:

• chr7-128199601-A-C
• rs12538332
• ENST00000710955.1:n.306-6088A>C

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-6088A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,086 control chromosomes in the GnomAD database, including 4,967 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 (4967 hom., cov: 32)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.275 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
ENSG00000292309	ENST00000710955.1	n.306-6088A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37975 AN: 151968 Hom.: 4966 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.250 AC: 37982 AN: 152086 Hom.: 4967 Cov.: 32 AF XY: 0.251 AC XY: 18664 AN XY: 74348

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.250

Alfa AF: 0.266 Hom.: 4186

Bravo AF: 0.239

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12538332; hg19: chr7-127839654;