rs6735174

Variant names:

• chr2-217035557-A-C
• rs6735174
• ENST00000695932.1:n.509+41539A>C

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+41539A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,148 control chromosomes in the GnomAD database, including 1,462 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 0.13 (1462 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 8 publications found

Genes affected

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

LOC105373874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000695932.1. 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	ENST00000695932.1		n.509+41539A>C		intron	N/A
	TESHL	ENST00000695934.1		n.172+41539A>C		intron	N/A
	TESHL	ENST00000695937.1		n.222-1656A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20446 AN: 152030 Hom.: 1463 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152148 Hom.: 1462 Cov.: 32 AF XY: 0.134 AC XY: 9963 AN XY: 74366

African (AFR) AF: 0.121 AC: 5018 AN: 41524

American (AMR) AF: 0.102 AC: 1567 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3472

East Asian (EAS) AF: 0.0194 AC: 100 AN: 5160

South Asian (SAS) AF: 0.199 AC: 958 AN: 4814

European-Finnish (FIN) AF: 0.149 AC: 1578 AN: 10588

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10170 AN: 67984

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.150 Hom.: 3517

Bravo AF: 0.130

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.4
DANN	Benign	0.73
PhyloP100		0.30

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: rs6735174;

hg19: chr2-217900280;