6-33139974-T-G

Variant names:

• chr6-33139974-T-G
• rs6457721
• ENST00000454398.1:n.102+3250A>C

Variant summary

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

The NR_190905.1(LOC105375021):​n.212-225A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,134 control chromosomes in the GnomAD database, including 3,419 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 0.19 (3419 hom., cov: 33)
• Consequence: LOC105375021 NR_190905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 12 publications found

Genes affected

HLA-DPA3 (HGNC:19393): (major histocompatibility complex, class II, DP alpha 3 (pseudogene))

ENSG00000291111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_190905.1. 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
	LOC105375021	NR_190905.1		n.212-225A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA3	ENST00000454398.1	TSL:6	n.102+3250A>C		intron	N/A
	ENSG00000291111	ENST00000782892.1		n.430-1147T>G		intron	N/A
	ENSG00000291111	ENST00000782893.1		n.404-1147T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29630 AN: 152016 Hom.: 3406 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.195 AC: 29664 AN: 152134 Hom.: 3419 Cov.: 33 AF XY: 0.198 AC XY: 14747 AN XY: 74358

African (AFR) AF: 0.147 AC: 6113 AN: 41508

American (AMR) AF: 0.312 AC: 4766 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2472 AN: 5172

South Asian (SAS) AF: 0.134 AC: 646 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2377 AN: 10578

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12313 AN: 67988

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.193 Hom.: 9238

Bravo AF: 0.207

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.78
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs6457721; hg19: chr6-33107751;