rs13190937

Variant names:

• chr6-28443467-G-A
• rs13190937
• NM_001012455.2:c.-146C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-28443467-G-A
• chr6-28443467-G-T

Variant summary

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

The NM_001012455.2(ZSCAN23):​c.-146C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,174 control chromosomes in the GnomAD database, including 7,919 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 0.31 (7917 hom., cov: 33)
  • Exomes 𝑓: 0.29 (2 hom.)
• Consequence: ZSCAN23 NM_001012455.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 27 publications found

Genes affected

ZSCAN23 (HGNC:21193): (zinc finger and SCAN domain containing 23) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN23	NM_001012455.2	c.-146C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 4	ENST00000289788.5	NP_001012458.1
ZSCAN23	NM_001012455.2	c.-146C>T		5_prime_UTR_variant	Exon 1 of 4	ENST00000289788.5	NP_001012458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN23	ENST00000289788.5	c.-146C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 4	1	NM_001012455.2	ENSP00000289788.4
ZSCAN23	ENST00000289788.5	c.-146C>T		5_prime_UTR_variant	Exon 1 of 4	1	NM_001012455.2	ENSP00000289788.4

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47808 AN: 152032 Hom.: 7908 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.292 AC: 7 AN: 24 Hom.: 2 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 6 AN: 16

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.314 AC: 47850 AN: 152150 Hom.: 7917 Cov.: 33 AF XY: 0.306 AC XY: 22732 AN XY: 74400

African (AFR) AF: 0.392 AC: 16255 AN: 41500

American (AMR) AF: 0.285 AC: 4354 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5184

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2314 AN: 10590

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21117 AN: 67984

Other (OTH) AF: 0.332 AC: 700 AN: 2106

Alfa AF: 0.313 Hom.: 18230

Bravo AF: 0.328

Asia WGS AF: 0.181 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		1.2
PromoterAI		-0.18	Neutral
Mutation Taster		=299/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13190937; hg19: chr6-28411244;