NM_182499.4:c.142-1097A>G

Variant names:

• chr1-154519207-A-G
• rs6674171
• NM_182499.4:c.142-1097A>G

Variant summary

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

The NM_182499.4(TDRD10):​c.142-1097A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,232 control chromosomes in the GnomAD database, including 3,059 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 0.19 (3059 hom., cov: 33)
• Consequence: TDRD10 NM_182499.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 16 publications found

Genes affected

TDRD10 (HGNC:25316): (tudor domain containing 10) Predicted to enable RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182499.4. 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
	TDRD10	NM_182499.4	MANE Select	c.142-1097A>G		intron	N/A	NP_872305.3	Q5VZ19-2
	TDRD10	NM_001098475.2		c.142-1097A>G		intron	N/A	NP_001091945.1	Q5VZ19-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TDRD10	ENST00000368482.8	TSL:1 MANE Select	c.142-1097A>G		intron	N/A	ENSP00000357467.4	Q5VZ19-2
	TDRD10	ENST00000889281.1		c.217-1097A>G		intron	N/A	ENSP00000559340.1
	TDRD10	ENST00000368480.3	TSL:2	c.142-1097A>G		intron	N/A	ENSP00000357465.3	Q5VZ19-1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29211 AN: 152114 Hom.: 3053 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.192 AC: 29246 AN: 152232 Hom.: 3059 Cov.: 33 AF XY: 0.199 AC XY: 14788 AN XY: 74426

African (AFR) AF: 0.139 AC: 5767 AN: 41534

American (AMR) AF: 0.163 AC: 2492 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3472

East Asian (EAS) AF: 0.156 AC: 809 AN: 5186

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4826

European-Finnish (FIN) AF: 0.351 AC: 3711 AN: 10580

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

European-Non Finnish (NFE) AF: 0.207 AC: 14101 AN: 68026

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.194 Hom.: 3684

Bravo AF: 0.172

Asia WGS AF: 0.223 AC: 775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.4
DANN	Benign	0.58
PhyloP100		0.062
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6674171; hg19: chr1-154491683;