rs588981

Positions:

• chr6-167311508-A-G

Variant summary

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

The NM_018974.4(UNC93A):​c.1108+3598A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,928 control chromosomes in the GnomAD database, including 9,614 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 (9614 hom., cov: 34)
• Consequence: UNC93A NM_018974.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

UNC93A (HGNC:12570): (unc-93 homolog A) Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC93A	NM_018974.4	c.1108+3598A>G		intron_variant		ENST00000230256.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC93A	ENST00000230256.8	c.1108+3598A>G		intron_variant		1	NM_018974.4	P1
UNC93A	ENST00000366829.2	c.982+3598A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53495 AN: 151810 Hom.: 9614 Cov.: 34

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.352 AC: 53532 AN: 151928 Hom.: 9614 Cov.: 34 AF XY: 0.355 AC XY: 26336 AN XY: 74228

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.350

Alfa AF: 0.343 Hom.: 1081

Bravo AF: 0.345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.28

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: rs588981; hg19: chr6-167724996;