rs2640201

Variant names:

• chr19-23530476-C-G
• rs2640201
• ENST00000601935.5:c.227-2462G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-23530476-C-G
• chr19-23530476-C-T

Variant summary

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

The ENST00000601935.5(ZNF675):​c.227-2462G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,946 control chromosomes in the GnomAD database, including 22,331 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 0.54 (22331 hom., cov: 32)
• Consequence: ZNF675 ENST00000601935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 2 publications found

Genes affected

ZNF675 (HGNC:30768): (zinc finger protein 675) Enables ubiquitin protein ligase binding activity. Involved in several processes, including negative regulation of osteoclast differentiation; negative regulation of signal transduction; and regulation of transcription, DNA-templated. Located in nucleus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC105372337 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601935.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF675	ENST00000601935.5	TSL:1	c.227-2462G>C		intron	N/A	ENSP00000469379.1	M0QXU1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81445 AN: 151828 Hom.: 22308 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.537 AC: 81522 AN: 151946 Hom.: 22331 Cov.: 32 AF XY: 0.540 AC XY: 40090 AN XY: 74276

African (AFR) AF: 0.628 AC: 26009 AN: 41424

American (AMR) AF: 0.560 AC: 8558 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1503 AN: 3466

East Asian (EAS) AF: 0.657 AC: 3380 AN: 5144

South Asian (SAS) AF: 0.532 AC: 2559 AN: 4806

European-Finnish (FIN) AF: 0.507 AC: 5359 AN: 10576

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32520 AN: 67944

Other (OTH) AF: 0.489 AC: 1030 AN: 2108

Alfa AF: 0.349 Hom.: 852

Bravo AF: 0.540

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.92
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2640201; hg19: chr19-23713278;