rs2038864

Variant names:

• chr6-40301570-T-A
• rs2038864
• ENST00000737788.1:n.190+15698T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-40301570-T-A
• chr6-40301570-T-G

Variant summary

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

The ENST00000737788.1(TDRG1):​n.190+15698T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,152 control chromosomes in the GnomAD database, including 4,893 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 0.25 (4893 hom., cov: 33)
• Consequence: TDRG1 ENST00000737788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 2 publications found

Genes affected

TDRG1 (HGNC:43642): (testis development related 1) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000296324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TDRG1	ENST00000737788.1	n.190+15698T>A		intron_variant	Intron 1 of 2
TDRG1	ENST00000737789.1	n.193+15698T>A		intron_variant	Intron 1 of 1
ENSG00000296324	ENST00000738169.1	n.344-6581A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37958 AN: 152034 Hom.: 4888 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.250 AC: 37979 AN: 152152 Hom.: 4893 Cov.: 33 AF XY: 0.252 AC XY: 18711 AN XY: 74384

African (AFR) AF: 0.221 AC: 9181 AN: 41530

American (AMR) AF: 0.208 AC: 3176 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5156

South Asian (SAS) AF: 0.409 AC: 1972 AN: 4822

European-Finnish (FIN) AF: 0.230 AC: 2438 AN: 10594

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18037 AN: 67980

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.263 Hom.: 666

Bravo AF: 0.240

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.34
DANN	Benign	0.73
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2038864; hg19: chr6-40269309;