6-167283460-T-G

Position:

• chr6-167283460-T-G

Variant summary

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

The ENST00000503433.5(UNC93A):​c.-51-7979T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,174 control chromosomes in the GnomAD database, including 1,669 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 0.13 (1669 hom., cov: 32)
• Consequence: UNC93A ENST00000503433.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

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 (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC93A	XM_011535905.3	c.-51-7979T>G		intron_variant			XP_011534207.1
UNC93A	XM_011535906.3	c.-52+2299T>G		intron_variant			XP_011534208.1
UNC93A	XM_017010958.1	c.-51-7979T>G		intron_variant			XP_016866447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UNC93A	ENST00000503433.5	c.-51-7979T>G		intron_variant		2		ENSP00000421484.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19822 AN: 152056 Hom.: 1668 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.130 AC: 19833 AN: 152174 Hom.: 1669 Cov.: 32 AF XY: 0.136 AC XY: 10080 AN XY: 74384

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.125

Alfa AF: 0.142 Hom.: 2251

Bravo AF: 0.120

Asia WGS AF: 0.262 AC: 906 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	2.3
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3010558; hg19: chr6-167696948;