chr8-106059379-G-T

Variant names:

• chr8-106059379-G-T
• rs2059943
• ENST00000821412.1:n.1093C>A

Variant summary

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

The ENST00000821412.1(ZFPM2-AS1):​n.1093C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,996 control chromosomes in the GnomAD database, including 10,125 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 0.35 (10125 hom., cov: 32)
• Consequence: ZFPM2-AS1 ENST00000821412.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 3 publications found

Genes affected

ZFPM2-AS1 (HGNC:50698): (ZFPM2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFPM2-AS1	NR_125796.1	n.124-243C>A		intron_variant	Intron 1 of 7
ZFPM2-AS1	NR_125797.1	n.123+1002C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFPM2-AS1	ENST00000821412.1	n.1093C>A		non_coding_transcript_exon_variant	Exon 1 of 1
ZFPM2-AS1	ENST00000509144.2	n.63+1002C>A		intron_variant	Intron 1 of 3	3
ZFPM2-AS1	ENST00000520078.5	n.81+1002C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52961 AN: 151878 Hom.: 10114 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.349 AC: 53000 AN: 151996 Hom.: 10125 Cov.: 32 AF XY: 0.349 AC XY: 25945 AN XY: 74294

African (AFR) AF: 0.185 AC: 7669 AN: 41458

American (AMR) AF: 0.412 AC: 6305 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1915 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4638 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28142 AN: 67934

Other (OTH) AF: 0.406 AC: 856 AN: 2110

Alfa AF: 0.373 Hom.: 1900

Bravo AF: 0.341

Asia WGS AF: 0.386 AC: 1342 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.45
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs2059943; hg19: chr8-107071607;