rs35410698

chr6-33134085-G-Achr6-33134085-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_926703.3(LOC105375021):n.559C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0359 in 152,196 control chromosomes in the GnomAD database, including 169 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 0.036 (169 hom., cov: 32)
• Consequence: LOC105375021 XR_926703.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

LOC105375021 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0359 (5463/152196) while in subpopulation SAS AF= 0.0537 (259/4822). AF 95% confidence interval is 0.0483. There are 169 homozygotes in gnomad4. There are 2612 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 170 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375021	XR_926703.3	n.559C>T		non_coding_transcript_exon_variant	3/4
LOC105375021	XR_001744086.2	n.559C>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPA3	ENST00000454398.1	n.103-2743C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5460 AN: 152078 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0359 AC: 5463 AN: 152196 Hom.: 169 Cov.: 32 AF XY: 0.0351 AC XY: 2612 AN XY: 74414

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0460

Alfa AF: 0.0280 Hom.: 26

Bravo AF: 0.0340

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.5
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35410698; hg19: chr6-33101862;