12-91930196-A-G

Variant names:

• chr12-91930196-A-G
• rs12427267
• ENST00000812104.1:n.180+7095A>G

Variant summary

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

The ENST00000812104.1(ENSG00000305639):​n.180+7095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,936 control chromosomes in the GnomAD database, including 19,834 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 0.49 (19834 hom., cov: 32)
• Consequence: ENSG00000305639 ENST00000812104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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+7095A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74260 AN: 151818 Hom.: 19800 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.489 AC: 74345 AN: 151936 Hom.: 19834 Cov.: 32 AF XY: 0.487 AC XY: 36190 AN XY: 74266

African (AFR) AF: 0.721 AC: 29879 AN: 41440

American (AMR) AF: 0.457 AC: 6971 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1483 AN: 5156

South Asian (SAS) AF: 0.548 AC: 2639 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4153 AN: 10548

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26476 AN: 67932

Other (OTH) AF: 0.442 AC: 932 AN: 2110

Alfa AF: 0.429 Hom.: 39936

Bravo AF: 0.498

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.39
PhyloP100		0.023

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: rs12427267;

hg19: chr12-92323972;

COSMIC: COSV107990805;