rs10741243

Variant names:

• chr10-131149699-C-G
• rs10741243
• NM_174937.4:c.1035-3039G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-131149699-C-G
• chr10-131149699-C-T

Variant summary

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

The NM_174937.4(TCERG1L):​c.1035-3039G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,176 control chromosomes in the GnomAD database, including 53,056 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 0.82 (53056 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 21 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.1035-3039G>C		intron_variant	Intron 6 of 11	ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.1074-3039G>C		intron_variant	Intron 7 of 12		XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.1035-3039G>C		intron_variant	Intron 6 of 11	1	NM_174937.4	ENSP00000357631.4
TCERG1L	ENST00000483040.1	n.2897-3039G>C		intron_variant	Intron 6 of 11	5

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125160 AN: 152058 Hom.: 53028 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.823 AC: 125240 AN: 152176 Hom.: 53056 Cov.: 33 AF XY: 0.827 AC XY: 61529 AN XY: 74390

African (AFR) AF: 0.598 AC: 24818 AN: 41492

American (AMR) AF: 0.843 AC: 12897 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2918 AN: 3472

East Asian (EAS) AF: 0.883 AC: 4559 AN: 5164

South Asian (SAS) AF: 0.932 AC: 4492 AN: 4820

European-Finnish (FIN) AF: 0.914 AC: 9689 AN: 10602

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62991 AN: 68016

Other (OTH) AF: 0.853 AC: 1799 AN: 2110

Alfa AF: 0.904 Hom.: 34658

Bravo AF: 0.803

Asia WGS AF: 0.884 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.37
PhyloP100		0.63
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: rs10741243; hg19: chr10-132947962;