chr6-167294872-T-G

Position:

• chr6-167294872-T-G

Variant summary

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

The ENST00000230256.8(UNC93A):​c.269+174T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,842 control chromosomes in the GnomAD database, including 6,221 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 0.28 (6221 hom., cov: 31)
• Consequence: UNC93A ENST00000230256.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC93A	NM_018974.4	c.269+174T>G		intron_variant		ENST00000230256.8	NP_061847.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNC93A	ENST00000230256.8	c.269+174T>G		intron_variant		1	NM_018974.4	ENSP00000230256	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42203 AN: 151724 Hom.: 6216 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.278 AC: 42246 AN: 151842 Hom.: 6221 Cov.: 31 AF XY: 0.274 AC XY: 20347 AN XY: 74210

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.276

Alfa AF: 0.222 Hom.: 1458

Bravo AF: 0.283

Asia WGS AF: 0.262 AC: 913 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	1.9
DANN	Benign	0.64

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: rs2076008; hg19: chr6-167708360;