chr2-217043749-A-G

Variant names:

• chr2-217043749-A-G
• rs10490444
• ENST00000695932.1:n.509+49731A>G

Variant summary

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

The ENST00000695932.1(TESHL):​n.509+49731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,062 control chromosomes in the GnomAD database, including 12,718 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 0.40 (12718 hom., cov: 32)
• Consequence: TESHL ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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

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
	TESHL	ENST00000695932.1		n.509+49731A>G		intron	N/A
	TESHL	ENST00000695934.1		n.172+49731A>G		intron	N/A
	TESHL	ENST00000695937.1		n.289+6469A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60993 AN: 151944 Hom.: 12705 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.401 AC: 61048 AN: 152062 Hom.: 12718 Cov.: 32 AF XY: 0.392 AC XY: 29132 AN XY: 74328

African (AFR) AF: 0.471 AC: 19526 AN: 41476

American (AMR) AF: 0.332 AC: 5073 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3472

East Asian (EAS) AF: 0.102 AC: 529 AN: 5188

South Asian (SAS) AF: 0.379 AC: 1827 AN: 4818

European-Finnish (FIN) AF: 0.294 AC: 3104 AN: 10560

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27997 AN: 67954

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.400 Hom.: 24010

Bravo AF: 0.406

Asia WGS AF: 0.248 AC: 862 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	0.49
DANN	Benign	0.53
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10490444; hg19: chr2-217908472;