rs12610873

Variant names:

• chr19-13831773-G-A
• rs12610873
• NM_001367834.3:c.*723G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-13831773-G-A
• chr19-13831773-G-C

Variant summary

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

The NM_001367834.3(ZSWIM4):​c.*723G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,106 control chromosomes in the GnomAD database, including 8,556 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 0.33 (8534 hom., cov: 29)
  • Exomes 𝑓: 0.40 (22 hom.)
• Consequence: ZSWIM4 NM_001367834.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 5 publications found

Genes affected

ZSWIM4 (HGNC:25704): (zinc finger SWIM-type containing 4) Predicted to enable zinc ion binding activity. Predicted to be part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

MIR23AHG (HGNC:27620): (miR-23a/27a/24-2 cluster host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM4	NM_001367834.3	c.*723G>A		3_prime_UTR_variant	Exon 14 of 14	ENST00000590508.6	NP_001354763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM4	ENST00000590508.6	c.*723G>A		3_prime_UTR_variant	Exon 14 of 14	2	NM_001367834.3	ENSP00000468285.2
MIR23AHG	ENST00000587762.2	n.11156C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ZSWIM4	ENST00000254323.6	c.*723G>A		3_prime_UTR_variant	Exon 13 of 13	2		ENSP00000254323.2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50567 AN: 151646 Hom.: 8532 Cov.: 29

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.398 AC: 137 AN: 344 Hom.: 22 Cov.: 0 AF XY: 0.399 AC XY: 87 AN XY: 218

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

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

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.406 AC: 121 AN: 298

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.321 AC: 9 AN: 28

Other (OTH) AF: 0.500 AC: 5 AN: 10

GnomAD4 genome AF: 0.333 AC: 50586 AN: 151762 Hom.: 8534 Cov.: 29 AF XY: 0.332 AC XY: 24625 AN XY: 74114

African (AFR) AF: 0.393 AC: 16268 AN: 41406

American (AMR) AF: 0.293 AC: 4470 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1215 AN: 5128

South Asian (SAS) AF: 0.321 AC: 1543 AN: 4806

European-Finnish (FIN) AF: 0.370 AC: 3896 AN: 10534

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21452 AN: 67872

Other (OTH) AF: 0.274 AC: 577 AN: 2108

Alfa AF: 0.318 Hom.: 20046

Bravo AF: 0.325

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.63
DANN	Benign	0.83
PhyloP100		-0.62
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: rs12610873; hg19: chr19-13942587; COSMIC: COSV54323712; COSMIC: COSV54323712;