rs2945988

Variant names:

• chr19-36519650-C-G
• rs2945988
• NM_001166037.2:c.-461-3951G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-36519650-C-G
• chr19-36519650-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001166037.2(ZNF260):​c.-461-3951G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZNF260 NM_001166037.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 9 publications found

Genes affected

ZNF260 (HGNC:13499): (zinc finger protein 260) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF260	NM_001166037.2	c.-461-3951G>C		intron_variant	Intron 2 of 2	ENST00000523638.6	NP_001159509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF260	ENST00000523638.6	c.-461-3951G>C		intron_variant	Intron 2 of 2	2	NM_001166037.2	ENSP00000429803.1
ZNF260	ENST00000588993.1	c.-569-2257G>C		intron_variant	Intron 1 of 2	1		ENSP00000467219.1
ZNF260	ENST00000592282.1	c.-575-1507G>C		intron_variant	Intron 2 of 3	1		ENSP00000464964.1
ZNF260	ENST00000593142.5	c.-461-3951G>C		intron_variant	Intron 1 of 1	1		ENSP00000465834.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 49651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.092
DANN	Benign	0.58
PhyloP100		-1.9

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: rs2945988; hg19: chr19-37010552;