rs12936911

Variant names:

• chr17-78332197-C-T
• rs12936911
• ENST00000586321.1:n.61-11768C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000586321.1(ENSG00000267737):​n.61-11768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 152,090 control chromosomes in the GnomAD database, including 13 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 0.010 (13 hom., cov: 31)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 1 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0103 (1565/152090) while in subpopulation NFE AF = 0.0176 (1196/67984). AF 95% confidence interval is 0.0168. There are 13 homozygotes in GnomAd4. There are 735 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 13 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371912	NR_188632.1		n.74-11768C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000586321.1	TSL:3	n.61-11768C>T		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.39-11768C>T		intron	N/A
	ENSG00000267737	ENST00000823931.1		n.72-11768C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0103 AC: 1565 AN: 151972 Hom.: 13 Cov.: 31

Gnomad AFR AF: 0.00237

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.00701

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.00604

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.00914

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

GnomAD4 genome AF: 0.0103 AC: 1565 AN: 152090 Hom.: 13 Cov.: 31 AF XY: 0.00989 AC XY: 735 AN XY: 74346

African (AFR) AF: 0.00236 AC: 98 AN: 41524

American (AMR) AF: 0.00700 AC: 107 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.000196 AC: 1 AN: 5106

South Asian (SAS) AF: 0.00332 AC: 16 AN: 4818

European-Finnish (FIN) AF: 0.00604 AC: 64 AN: 10598

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0176 AC: 1196 AN: 67984

Other (OTH) AF: 0.00905 AC: 19 AN: 2100

Alfa AF: 0.0147 Hom.: 11

Bravo AF: 0.0110

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.85
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs12936911; hg19: chr17-76328278;