chr12-18782908-T-C

Variant names:

• chr12-18782908-T-C
• rs11834116
• ENST00000838343.1:n.136+9518T>C

Variant summary

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

The ENST00000838343.1(ENSG00000309085):​n.136+9518T>C variant causes a intron change. The variant allele was found at a frequency of 0.164 in 152,114 control chromosomes in the GnomAD database, including 2,269 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 0.16 (2269 hom., cov: 32)
• Consequence: ENSG00000309085 ENST00000838343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

Genes affected

ENSG00000309085 (HGNC:58983):

LOC102724227 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838343.1. 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
	ENSG00000309085	ENST00000838343.1		n.136+9518T>C		intron	N/A
	ENSG00000309085	ENST00000838344.1		n.119+9518T>C		intron	N/A
	ENSG00000309085	ENST00000838345.1		n.127+9518T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24956 AN: 151996 Hom.: 2261 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.164 AC: 24990 AN: 152114 Hom.: 2269 Cov.: 32 AF XY: 0.161 AC XY: 12000 AN XY: 74348

African (AFR) AF: 0.204 AC: 8458 AN: 41500

American (AMR) AF: 0.127 AC: 1940 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2164 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10923 AN: 67962

Other (OTH) AF: 0.164 AC: 348 AN: 2116

Alfa AF: 0.123 Hom.: 759

Bravo AF: 0.162

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.45

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: rs11834116;

hg19: chr12-18935842;