12-27330906-G-C

Variant names:

• chr12-27330906-G-C
• rs7137588
• ENST00000806970.1:n.249+1716C>G

Variant summary

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

The ENST00000806970.1(ENSG00000304890):​n.249+1716C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,966 control chromosomes in the GnomAD database, including 7,372 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 0.30 (7372 hom., cov: 31)
• Consequence: ENSG00000304890 ENST00000806970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 7 publications found

Genes affected

ENSG00000304890 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806970.1. 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
	ENSG00000304890	ENST00000806970.1		n.249+1716C>G		intron	N/A
	ENSG00000304890	ENST00000806971.1		n.233+1716C>G		intron	N/A
	ENSG00000304890	ENST00000806972.1		n.193+1716C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45006 AN: 151848 Hom.: 7368 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.296 AC: 45045 AN: 151966 Hom.: 7372 Cov.: 31 AF XY: 0.292 AC XY: 21696 AN XY: 74252

African (AFR) AF: 0.197 AC: 8166 AN: 41446

American (AMR) AF: 0.223 AC: 3408 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3472

East Asian (EAS) AF: 0.101 AC: 522 AN: 5168

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4810

European-Finnish (FIN) AF: 0.351 AC: 3707 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25833 AN: 67946

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.225 Hom.: 623

Bravo AF: 0.277

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.12

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: rs7137588;

hg19: chr12-27483839;