rs10765037

Variant names:

• chr10-131134207-G-A
• rs10765037
• NM_174937.4:c.1259+172C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-131134207-G-A
• chr10-131134207-G-C

Variant summary

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

The NM_174937.4(TCERG1L):​c.1259+172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,086 control chromosomes in the GnomAD database, including 5,507 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 0.26 (5507 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 1 publications found

Genes affected

TCERG1L (HGNC:23533): (transcription elongation regulator 1 like) Predicted to enable RNA polymerase binding activity and transcription coregulator activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174937.4. 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
	TCERG1L	NM_174937.4	MANE Select	c.1259+172C>T		intron	N/A	NP_777597.2	Q5VWI1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	ENST00000368642.4	TSL:1 MANE Select	c.1259+172C>T		intron	N/A	ENSP00000357631.4	Q5VWI1
	TCERG1L	ENST00000935680.1		c.1298+172C>T		intron	N/A	ENSP00000605739.1
	TCERG1L	ENST00000483040.1	TSL:5	n.3121+172C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40192 AN: 151966 Hom.: 5508 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.264 AC: 40216 AN: 152086 Hom.: 5507 Cov.: 33 AF XY: 0.268 AC XY: 19884 AN XY: 74328

African (AFR) AF: 0.178 AC: 7369 AN: 41492

American (AMR) AF: 0.310 AC: 4736 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3472

East Asian (EAS) AF: 0.296 AC: 1527 AN: 5162

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4814

European-Finnish (FIN) AF: 0.321 AC: 3392 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19488 AN: 67960

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.166 Hom.: 354

Bravo AF: 0.257

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.51
PhyloP100		-1.8
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: rs10765037; hg19: chr10-132932470;