10-96133669-G-A

Variant names:

• chr10-96133669-G-A
• rs2446024
• NM_001330736.2:c.-302+21G>A

Variant summary

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

The NM_001330736.2(ZNF518A):​c.-302+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,176 control chromosomes in the GnomAD database, including 60,511 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 0.89 (60510 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ZNF518A NM_001330736.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 3 publications found

Genes affected

ZNF518A (HGNC:29009): (zinc finger protein 518A) The protein encoded by this gene is a member of the krueppel C2H2-type zinc finger protein family. The encoded protein contains five zinc fingers and is likely a nuclear transcriptional regulator. Numerous transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2016]

LOC124902486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330736.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF518A	NM_001330736.2	MANE Select	c.-302+21G>A		intron	N/A	NP_001317665.1
	ZNF518A	NM_001278524.2		c.-475+21G>A		intron	N/A	NP_001265453.1
	ZNF518A	NM_001278525.2		c.-324+21G>A		intron	N/A	NP_001265454.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF518A	ENST00000316045.10	TSL:1 MANE Select	c.-302+21G>A		intron	N/A	ENSP00000479684.1
	ZNF518A	ENST00000624776.4	TSL:1	c.-324+21G>A		intron	N/A	ENSP00000485614.1
	ZNF518A	ENST00000614149.2	TSL:5	c.-402+21G>A		intron	N/A	ENSP00000481657.1

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135133 AN: 152056 Hom.: 60468 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.893

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.889 AC: 135237 AN: 152174 Hom.: 60510 Cov.: 31 AF XY: 0.888 AC XY: 66081 AN XY: 74402

African (AFR) AF: 0.781 AC: 32412 AN: 41490

American (AMR) AF: 0.860 AC: 13153 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3094 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4491 AN: 5178

South Asian (SAS) AF: 0.853 AC: 4114 AN: 4824

European-Finnish (FIN) AF: 0.957 AC: 10144 AN: 10600

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64805 AN: 68002

Other (OTH) AF: 0.895 AC: 1893 AN: 2114

Alfa AF: 0.908 Hom.: 10882

Bravo AF: 0.877

Asia WGS AF: 0.878 AC: 3054 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.33
PhyloP100		0.60

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: rs2446024; hg19: chr10-97893426;