chr19-36519650-C-T

Variant names:

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

Variant summary

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

The NM_001166037.2(ZNF260):​c.-461-3951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,972 control chromosomes in the GnomAD database, including 29,956 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 0.62 (29956 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94428 AN: 151854 Hom.: 29929 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.622 AC: 94515 AN: 151972 Hom.: 29956 Cov.: 32 AF XY: 0.618 AC XY: 45932 AN XY: 74302

African (AFR) AF: 0.642 AC: 26599 AN: 41446

American (AMR) AF: 0.528 AC: 8072 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4820

European-Finnish (FIN) AF: 0.670 AC: 7059 AN: 10536

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.653 AC: 44347 AN: 67944

Other (OTH) AF: 0.600 AC: 1264 AN: 2108

Alfa AF: 0.633 Hom.: 49651

Bravo AF: 0.608

Asia WGS AF: 0.503 AC: 1746 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.54
PhyloP100		-1.9
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: rs2945988; hg19: chr19-37010552;