rs7762056

Variant names:

• chr6-40302308-C-A
• rs7762056
• ENST00000737788.1:n.190+16436C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-40302308-C-A
• chr6-40302308-C-T

Variant summary

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

The ENST00000737788.1(TDRG1):​n.190+16436C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,142 control chromosomes in the GnomAD database, including 4,866 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 (4866 hom., cov: 33)
• Consequence: TDRG1 ENST00000737788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737788.1. 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
	TDRG1	ENST00000737788.1		n.190+16436C>A		intron	N/A
	TDRG1	ENST00000737789.1		n.193+16436C>A		intron	N/A
	ENSG00000296324	ENST00000738169.1		n.343+6189G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37834 AN: 152024 Hom.: 4861 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 152142 Hom.: 4866 Cov.: 33 AF XY: 0.251 AC XY: 18654 AN XY: 74382

African (AFR) AF: 0.219 AC: 9077 AN: 41524

American (AMR) AF: 0.208 AC: 3183 AN: 15294

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

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5164

South Asian (SAS) AF: 0.408 AC: 1969 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2429 AN: 10584

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

European-Non Finnish (NFE) AF: 0.265 AC: 18028 AN: 67976

Other (OTH) AF: 0.267 AC: 562 AN: 2104

Alfa AF: 0.255 Hom.: 14118

Bravo AF: 0.239

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7762056; hg19: chr6-40270047;