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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305639	ENST00000812104.1		n.180+9623T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11106345;

hg19: chr12-92326500;