chr2-71298655-T-C

Variant names:

• chr2-71298655-T-C
• rs12612930
• ENST00000410075.6:c.116+21901T>C

Variant summary

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

The ENST00000410075.6(ZNF638):​c.116+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 ENST00000410075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF638	ENST00000410075.6	c.116+21901T>C		intron_variant	Intron 1 of 12	1		ENSP00000485608.2
ZNF638	ENST00000466975.6	c.116+21901T>C		intron_variant	Intron 1 of 25	4		ENSP00000485154.2
ZNF638	ENST00000466330.5	c.-85+21901T>C		intron_variant	Intron 1 of 5	3		ENSP00000485494.1

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

African (AFR) AF: 0.0117 AC: 488 AN: 41576

American (AMR) AF: 0.0839 AC: 1283 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2900 AN: 5168

South Asian (SAS) AF: 0.0853 AC: 412 AN: 4832

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1808 AN: 68016

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0435 Hom.: 1010

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
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs12612930; hg19: chr2-71525785;