rs12612930

chr2-71298655-T-Cchr2-71298655-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000410075.5(ZNF638):c.-203+21901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,276 control chromosomes in the GnomAD database, including 976 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 0.053 (976 hom., cov: 32)
• Consequence: ZNF638 ENST00000410075.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

ZNF638 (HGNC:17894): (zinc finger protein 638) The protein encoded by this gene is a nucleoplasmic protein. It binds cytidine-rich sequences in double-stranded DNA. This protein has three types of domains: MH1, MH2 (repeated three times) and MH3. It is associated with packaging, transferring, or processing transcripts. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF638	ENST00000410075.5	c.-203+21901T>C		intron_variant		1
ZNF638	ENST00000466330.5	c.-85+21901T>C		intron_variant		3
ZNF638	ENST00000466975.5	c.116+21901T>C		intron_variant		4
ZNF638	ENST00000494621.5	c.-217+21901T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0525 AC: 7991 AN: 152158 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0525 AC: 8001 AN: 152276 Hom.: 976 Cov.: 32 AF XY: 0.0590 AC XY: 4391 AN XY: 74472

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.0839

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0366 Hom.: 35

Bravo AF: 0.0569

Asia WGS AF: 0.287 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	12
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12612930; hg19: chr2-71525785;