rs16912392

Variant names:

• chr11-13189661-C-A
• rs16912392
• ENST00000741297.1:n.95-8150G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-13189661-C-A
• chr11-13189661-C-T

Variant summary

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

The ENST00000741297.1(ENSG00000296717):​n.95-8150G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,044 control chromosomes in the GnomAD database, including 2,743 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 0.18 (2743 hom., cov: 32)
• Consequence: ENSG00000296717 ENST00000741297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 4 publications found

Genes affected

ENSG00000296717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741297.1. 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
	ENSG00000296717	ENST00000741297.1		n.95-8150G>T		intron	N/A
	ENSG00000296717	ENST00000741299.1		n.80-8150G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28009 AN: 151926 Hom.: 2743 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.184 AC: 28031 AN: 152044 Hom.: 2743 Cov.: 32 AF XY: 0.187 AC XY: 13901 AN XY: 74342

African (AFR) AF: 0.153 AC: 6331 AN: 41482

American (AMR) AF: 0.231 AC: 3522 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3466

East Asian (EAS) AF: 0.0570 AC: 295 AN: 5178

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2253 AN: 10546

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13126 AN: 67962

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.192 Hom.: 12416

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.40
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs16912392; hg19: chr11-13211208;