chr17-50203294-GA-G

Variant names:

• chr17-50203294-GA-G
• rs11327935
• ENST00000509943.2:n.59+3361delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000509943.2(TILAM):​n.59+3361delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 2,574 homozygotes. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.18 (2574 hom., cov: 28)
• Consequence: TILAM ENST00000509943.2 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0550
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TILAM	ENST00000509943.2	TSL:3	n.59+3361delA		intron	N/A
	TILAM	ENST00000832079.1		n.155+2049delA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27336 AN: 151726 Hom.: 2572 Cov.: 28

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.180 AC: 27347 AN: 151846 Hom.: 2574 Cov.: 28 AF XY: 0.175 AC XY: 12951 AN XY: 74196

African (AFR) AF: 0.193 AC: 7988 AN: 41356

American (AMR) AF: 0.164 AC: 2497 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3466

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5158

South Asian (SAS) AF: 0.128 AC: 616 AN: 4814

European-Finnish (FIN) AF: 0.145 AC: 1530 AN: 10550

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13380 AN: 67916

Other (OTH) AF: 0.196 AC: 414 AN: 2116

Alfa AF: 0.0595 Hom.: 77

Bravo AF: 0.181

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Bone mineral density variation quantitative trait locus (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs11327935; hg19: chr17-48280655;