rs1177749

Variant names:

• chr10-96138234-G-A
• rs1177749
• NM_001330736.2:c.-302+4586G>A

Your query was ambiguous. Multiple possible variants found:

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

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+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
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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+4586G>A		intron	N/A	NP_001317665.1
	ZNF518A	NM_001278524.2		c.-475+4586G>A		intron	N/A	NP_001265453.1
	ZNF518A	NM_001278525.2		c.-324+4586G>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+4586G>A		intron	N/A	ENSP00000479684.1
	ZNF518A	ENST00000624776.4	TSL:1	c.-324+4586G>A		intron	N/A	ENSP00000485614.1
	ZNF518A	ENST00000614149.2	TSL:5	c.-402+4586G>A		intron	N/A	ENSP00000481657.1

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

African (AFR) AF: 0.148 AC: 6146 AN: 41486

American (AMR) AF: 0.316 AC: 4832 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3435 AN: 5162

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4816

European-Finnish (FIN) AF: 0.444 AC: 4682 AN: 10550

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23752 AN: 67948

Other (OTH) AF: 0.291 AC: 616 AN: 2116

Alfa AF: 0.325 Hom.: 2728

Bravo AF: 0.289

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-0.51
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

Other links and lift over

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