rs12644822

Variant names:

• chr4-67756817-G-A
• rs12644822
• ENST00000500538.7:n.1987+1562G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-67756817-G-A
• chr4-67756817-G-C

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.1987+1562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,998 control chromosomes in the GnomAD database, including 8,599 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 0.33 (8599 hom., cov: 31)
• Consequence: UBA6-DT ENST00000500538.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 8 publications found

Genes affected

UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.1987+1562G>A		intron_variant	Intron 6 of 7	1
UBA6-DT	ENST00000502758.1	n.483+1562G>A		intron_variant	Intron 5 of 5	4
UBA6-DT	ENST00000660972.1	n.1357+1562G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50433 AN: 151880 Hom.: 8594 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.332 AC: 50444 AN: 151998 Hom.: 8599 Cov.: 31 AF XY: 0.333 AC XY: 24732 AN XY: 74290

African (AFR) AF: 0.255 AC: 10551 AN: 41442

American (AMR) AF: 0.308 AC: 4703 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1561 AN: 5154

South Asian (SAS) AF: 0.347 AC: 1671 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4257 AN: 10554

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25076 AN: 67970

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.325 Hom.: 1352

Bravo AF: 0.323

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs12644822; hg19: chr4-68622535;