rs750754013

Variant names:

• chr11-63764893-C-G
• NM_001144936.2:c.999G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-63764893-C-G
• chr11-63764893-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001144936.2(ZFTA):​c.999G>C​(p.Leu333Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000731 in 1,367,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L333L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: ZFTA NM_001144936.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

ZFTA (HGNC:28449): (zinc finger translocation associated) Predicted to be involved in negative regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP7: Synonymous conserved (PhyloP=-0.003 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFTA	NM_001144936.2	c.999G>C	p.Leu333Leu	synonymous_variant	Exon 3 of 5	ENST00000433688.2	NP_001138408.1
ZFTA	XM_047427478.1	c.999G>C	p.Leu333Leu	synonymous_variant	Exon 3 of 4		XP_047283434.1
ZFTA	XM_047427477.1	c.638-295G>C		intron_variant	Intron 2 of 3		XP_047283433.1
ZFTA	XM_024448662.2	c.637+914G>C		intron_variant	Intron 2 of 2		XP_024304430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFTA	ENST00000433688.2	c.999G>C	p.Leu333Leu	synonymous_variant	Exon 3 of 5	5	NM_001144936.2	ENSP00000482180.1
ZFTA	ENST00000338498.6	c.154+914G>C		intron_variant	Intron 1 of 1	1		ENSP00000483097.1
ZFTA	ENST00000445014.3	c.384G>C	p.Leu128Leu	synonymous_variant	Exon 3 of 4	5		ENSP00000478462.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.31e-7 AC: 1 AN: 1367252 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 672558

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.37e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.4
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-63532365;