rs16856795

Variant names:

• chr2-216988435-T-C
• rs16856795
• ENST00000447289.1:n.511-5523T>C

Variant summary

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

The ENST00000607591.1(TESHL):​n.273-5523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 152,304 control chromosomes in the GnomAD database, including 245 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 0.040 (245 hom., cov: 32)
• Consequence: TESHL ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 1 publications found

Genes affected

TESHL (HGNC:52740): (testicular germ cell expressed HSF2 interacting lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607591.1. 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
	TESHL	ENST00000447289.1	TSL:5	n.511-5523T>C		intron	N/A
	TESHL	ENST00000607591.1	TSL:3	n.273-5523T>C		intron	N/A
	TESHL	ENST00000695932.1		n.449-5523T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6075 AN: 152186 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0400 AC: 6093 AN: 152304 Hom.: 245 Cov.: 32 AF XY: 0.0413 AC XY: 3078 AN XY: 74458

African (AFR) AF: 0.0430 AC: 1787 AN: 41556

American (AMR) AF: 0.126 AC: 1931 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3468

East Asian (EAS) AF: 0.0969 AC: 502 AN: 5182

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4824

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10622

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0198 AC: 1347 AN: 68036

Other (OTH) AF: 0.0411 AC: 87 AN: 2116

Alfa AF: 0.0317 Hom.: 413

Bravo AF: 0.0515

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism

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: rs16856795;

hg19: chr2-217853158;