12-91932724-T-C

Variant names:

• chr12-91932724-T-C
• rs11106345
• ENST00000812104.1:n.180+9623T>C

Variant summary

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

The ENST00000812104.1(ENSG00000305639):​n.180+9623T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,806 control chromosomes in the GnomAD database, including 25,705 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 0.57 (25705 hom., cov: 32)
• Consequence: ENSG00000305639 ENST00000812104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 2 publications found

Genes affected

ENSG00000305639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369901	XR_007063580.1	n.842-3373A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305639	ENST00000812104.1	n.180+9623T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86243 AN: 151688 Hom.: 25698 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.568 AC: 86280 AN: 151806 Hom.: 25705 Cov.: 32 AF XY: 0.571 AC XY: 42393 AN XY: 74216

African (AFR) AF: 0.386 AC: 16013 AN: 41440

American (AMR) AF: 0.572 AC: 8705 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2317 AN: 3460

East Asian (EAS) AF: 0.893 AC: 4607 AN: 5158

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4822

European-Finnish (FIN) AF: 0.646 AC: 6830 AN: 10576

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43286 AN: 67820

Other (OTH) AF: 0.611 AC: 1286 AN: 2106

Alfa AF: 0.613 Hom.: 16688

Bravo AF: 0.561

Asia WGS AF: 0.675 AC: 2342 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.90
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs11106345; hg19: chr12-92326500;