rs754575

Variant names:

• chr10-131237795-T-C
• rs754575
• NM_174937.4:c.856+22464A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-131237795-T-C
• chr10-131237795-T-G

Variant summary

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

The NM_174937.4(TCERG1L):​c.856+22464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,008 control chromosomes in the GnomAD database, including 9,355 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 0.34 (9355 hom., cov: 32)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	NM_174937.4	MANE Select	c.856+22464A>G		intron	N/A	NP_777597.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	ENST00000368642.4	TSL:1 MANE Select	c.856+22464A>G		intron	N/A	ENSP00000357631.4
	TCERG1L	ENST00000483040.1	TSL:5	n.78+22464A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51212 AN: 151890 Hom.: 9334 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.337 AC: 51272 AN: 152008 Hom.: 9355 Cov.: 32 AF XY: 0.335 AC XY: 24916 AN XY: 74284

African (AFR) AF: 0.492 AC: 20391 AN: 41452

American (AMR) AF: 0.336 AC: 5137 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1803 AN: 5152

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4814

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17728 AN: 67960

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.295 Hom.: 19042

Bravo AF: 0.351

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.37
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: rs754575; hg19: chr10-133036058;