rs10509700

chr10-96134774-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330736.2(ZNF518A):c.-302+1126G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,102 control chromosomes in the GnomAD database, including 11,884 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 0.37 (11884 hom., cov: 33)
• Consequence: ZNF518A NM_001330736.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF518A	NM_001330736.2	c.-302+1126G>C		intron_variant		ENST00000316045.10
LOC124902486	XR_007062254.1	n.13956C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF518A	ENST00000316045.10	c.-302+1126G>C		intron_variant		1	NM_001330736.2	P1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56477 AN: 151984 Hom.: 11887 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.371 AC: 56488 AN: 152102 Hom.: 11884 Cov.: 33 AF XY: 0.365 AC XY: 27155 AN XY: 74352

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.393

Alfa AF: 0.426 Hom.: 1920

Bravo AF: 0.364

Asia WGS AF: 0.138 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.42
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509700; hg19: chr10-97894531;