17-50203629-A-C

Variant names:

• chr17-50203629-A-C
• rs1107946
• ENST00000509943.2:n.59+3695A>C

Variant summary

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

The ENST00000509943.2(TILAM):​n.59+3695A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,072 control chromosomes in the GnomAD database, including 48,695 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 0.80 (48695 hom., cov: 31)
• Consequence: TILAM ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 79 publications found

Genes affected

TILAM (HGNC:52795): (long intergenic non-protein coding RNA 1969)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509943.2. 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
	TILAM	ENST00000509943.2	TSL:3	n.59+3695A>C		intron	N/A
	TILAM	ENST00000832079.1		n.155+2383A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121002 AN: 151956 Hom.: 48667 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.796 AC: 121084 AN: 152072 Hom.: 48695 Cov.: 31 AF XY: 0.793 AC XY: 58955 AN XY: 74344

African (AFR) AF: 0.697 AC: 28849 AN: 41416

American (AMR) AF: 0.751 AC: 11482 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3558 AN: 5168

South Asian (SAS) AF: 0.732 AC: 3519 AN: 4810

European-Finnish (FIN) AF: 0.875 AC: 9280 AN: 10600

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58540 AN: 67998

Other (OTH) AF: 0.802 AC: 1693 AN: 2110

Alfa AF: 0.830 Hom.: 7643

Bravo AF: 0.783

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.60
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1107946; hg19: chr17-48280990;