rs12111032

Variant names:

• chr6-31274414-A-G
• rs12111032
• ENST00000755297.1:n.32+3308A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+3308A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 150,894 control chromosomes in the GnomAD database, including 4,429 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 0.24 (4429 hom., cov: 27)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 18 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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
ENSG00000298396	ENST00000755297.1	n.32+3308A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35635 AN: 150774 Hom.: 4421 Cov.: 27

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.236 AC: 35652 AN: 150894 Hom.: 4429 Cov.: 27 AF XY: 0.240 AC XY: 17697 AN XY: 73616

African (AFR) AF: 0.189 AC: 7755 AN: 41038

American (AMR) AF: 0.223 AC: 3389 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3460

East Asian (EAS) AF: 0.351 AC: 1789 AN: 5094

South Asian (SAS) AF: 0.280 AC: 1333 AN: 4768

European-Finnish (FIN) AF: 0.282 AC: 2902 AN: 10276

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17100 AN: 67784

Other (OTH) AF: 0.194 AC: 408 AN: 2100

Alfa AF: 0.248 Hom.: 5674

Bravo AF: 0.228

Asia WGS AF: 0.300 AC: 1043 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.77
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs12111032; hg19: chr6-31242191;