rs1177749

Positions:

• chr10-96138234-G-A
• chr10-96138234-G-T

Variant summary

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

The NM_001330736.2(ZNF518A):​c.-302+4586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,026 control chromosomes in the GnomAD database, including 8,250 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 (8250 hom., cov: 32)
• Consequence: ZNF518A NM_001330736.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF518A	NM_001330736.2	c.-302+4586G>A		intron_variant		ENST00000316045.10	NP_001317665.1
LOC124902486	XR_007062254.1	n.10556C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF518A	ENST00000316045.10	c.-302+4586G>A		intron_variant		1	NM_001330736.2	ENSP00000479684	P1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46562 AN: 151906 Hom.: 8247 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46589 AN: 152026 Hom.: 8250 Cov.: 32 AF XY: 0.317 AC XY: 23569 AN XY: 74322

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.291

Alfa AF: 0.328 Hom.: 2721

Bravo AF: 0.289

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1177749; hg19: chr10-97897991; COSMIC: COSV60150084;