rs17006292

Variant names:

• chr2-121261187-C-A
• rs17006292
• NM_014553.3:c.215-11540G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-121261187-C-A
• chr2-121261187-C-T

Variant summary

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

The NM_014553.3(TFCP2L1):​c.215-11540G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 152,290 control chromosomes in the GnomAD database, including 143 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 0.028 (143 hom., cov: 33)
• Consequence: TFCP2L1 NM_014553.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 14 publications found

Genes affected

TFCP2L1 (HGNC:17925): (transcription factor CP2 like 1) Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and membrane. Predicted to be part of chromatin. 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFCP2L1	NM_014553.3	c.215-11540G>T		intron_variant	Intron 2 of 14	ENST00000263707.6	NP_055368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFCP2L1	ENST00000263707.6	c.215-11540G>T		intron_variant	Intron 2 of 14	1	NM_014553.3	ENSP00000263707.5

Frequencies

GnomAD3 genomes AF: 0.0277 AC: 4218 AN: 152172 Hom.: 142 Cov.: 33

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0288

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00285

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0279 AC: 4243 AN: 152290 Hom.: 143 Cov.: 33 AF XY: 0.0286 AC XY: 2126 AN XY: 74458

African (AFR) AF: 0.0842 AC: 3497 AN: 41550

American (AMR) AF: 0.0122 AC: 186 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.0289 AC: 150 AN: 5188

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00285 AC: 194 AN: 68034

Other (OTH) AF: 0.0246 AC: 52 AN: 2112

Alfa AF: 0.0132 Hom.: 148

Bravo AF: 0.0308

Asia WGS AF: 0.0290 AC: 101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.19
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: rs17006292; hg19: chr2-122018763;