rs12936911

Positions:

• chr17-78332197-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000586321.1(ENSG00000267737):​n.61-11768C>T variant causes a intron, non coding transcript 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: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586321.1	n.61-11768C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.00236

Gnomad4 AMR AF: 0.00700

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.00604

Gnomad4 NFE AF: 0.0176

Gnomad4 OTH AF: 0.00905

Alfa AF: 0.0143 Hom.: 9

Bravo AF: 0.0110

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12936911; hg19: chr17-76328278;