chr6-167294872-T-G

Variant names:

• chr6-167294872-T-G
• rs2076008
• NM_018974.4:c.269+174T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018974.4(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 NM_018974.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 6 publications found

Genes affected

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

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 = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018974.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNC93A	NM_018974.4	MANE Select	c.269+174T>G		intron	N/A	NP_061847.2
	UNC93A	NM_001143947.2		c.269+174T>G		intron	N/A	NP_001137419.1	Q86WB7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UNC93A	ENST00000230256.8	TSL:1 MANE Select	c.269+174T>G		intron	N/A	ENSP00000230256.3	Q86WB7-1
	UNC93A	ENST00000366829.2	TSL:1	c.269+174T>G		intron	N/A	ENSP00000355794.2	Q86WB7-2
	UNC93A	ENST00000860147.1		c.269+174T>G		intron	N/A	ENSP00000530206.1

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

African (AFR) AF: 0.368 AC: 15210 AN: 41322

American (AMR) AF: 0.204 AC: 3119 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1930 AN: 5160

South Asian (SAS) AF: 0.198 AC: 957 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2234 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17006 AN: 67924

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.226 Hom.: 1694

Bravo AF: 0.283

Asia WGS AF: 0.262 AC: 913 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	1.9
DANN	Benign	0.64
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

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: rs2076008; hg19: chr6-167708360;