rs1583670

Variant names:

• chr10-131185951-T-C
• rs1583670
• NM_174937.4:c.857-19066A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174937.4(TCERG1L):​c.857-19066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,130 control chromosomes in the GnomAD database, including 41,678 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 0.72 (41678 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.857-19066A>G		intron_variant	Intron 4 of 11	ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.857-19066A>G		intron_variant	Intron 4 of 12		XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.857-19066A>G		intron_variant	Intron 4 of 11	1	NM_174937.4	ENSP00000357631.4
TCERG1L	ENST00000483040.1	n.79-19066A>G		intron_variant	Intron 1 of 11	5

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109241 AN: 152012 Hom.: 41679 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.718 AC: 109269 AN: 152130 Hom.: 41678 Cov.: 33 AF XY: 0.718 AC XY: 53365 AN XY: 74352

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.749

Alfa AF: 0.793 Hom.: 32259

Bravo AF: 0.699

Asia WGS AF: 0.755 AC: 2626 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	0.61
DANN	Benign	0.26

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

Publications

LitVar

Other links and lift over

dbSNP: rs1583670; hg19: chr10-132984214;