17-50202995-G-C

Variant names:

• chr17-50202995-G-C
• rs2269336
• ENST00000509943.2:n.59+3061G>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+3061G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,092 control chromosomes in the GnomAD database, including 3,189 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 0.19 (3189 hom., cov: 32)
• Consequence: TILAM ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 19 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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+3061G>C		intron	N/A
	TILAM	ENST00000832079.1		n.155+1749G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29122 AN: 151974 Hom.: 3185 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.192 AC: 29166 AN: 152092 Hom.: 3189 Cov.: 32 AF XY: 0.196 AC XY: 14559 AN XY: 74350

African (AFR) AF: 0.257 AC: 10636 AN: 41448

American (AMR) AF: 0.245 AC: 3753 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1937 AN: 5162

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1177 AN: 10606

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9360 AN: 67986

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.0678 Hom.: 93

Bravo AF: 0.205

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.93

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: rs2269336;

hg19: chr17-48280356;