rs1921987

Variant names:

• chr2-216957190-G-A
• rs1921987
• ENST00000447289.1:n.511-36768G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-216957190-G-A
• chr2-216957190-G-C
• chr2-216957190-G-T

Variant summary

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

The ENST00000607591.1(TESHL):​n.114-24781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,954 control chromosomes in the GnomAD database, including 8,372 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 0.31 (8372 hom., cov: 31)
• Consequence: TESHL ENST00000607591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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.511-36768G>A		intron	N/A
	TESHL	ENST00000607591.1	TSL:3	n.114-24781G>A		intron	N/A
	TESHL	ENST00000695932.1		n.449-36768G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47493 AN: 151838 Hom.: 8374 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.313 AC: 47497 AN: 151954 Hom.: 8372 Cov.: 31 AF XY: 0.317 AC XY: 23562 AN XY: 74260

African (AFR) AF: 0.150 AC: 6204 AN: 41460

American (AMR) AF: 0.361 AC: 5516 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3468

East Asian (EAS) AF: 0.234 AC: 1204 AN: 5154

South Asian (SAS) AF: 0.490 AC: 2358 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3942 AN: 10538

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25949 AN: 67938

Other (OTH) AF: 0.323 AC: 683 AN: 2116

Alfa AF: 0.361 Hom.: 5625

Bravo AF: 0.301

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1921987; hg19: chr2-217821913;