rs10751

Variant names:

• chr6-32934806-G-A
• rs10751
• NM_002118.5:c.*165C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32934806-G-A
• chr6-32934806-G-C
• chr6-32934806-G-T

Variant summary

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

The NM_002118.5(HLA-DMB):​c.*165C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 688,032 control chromosomes in the GnomAD database, including 6,804 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 (1323 hom., cov: 31)
  • Exomes 𝑓: 0.13 (5481 hom.)
• Consequence: HLA-DMB NM_002118.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 24 publications found

Genes affected

HLA-DMB (HGNC:4935): (major histocompatibility complex, class II, DM beta) HLA-DMB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta (DMB) chain, both anchored in the membrane. It is located in intracellular vesicles. DM plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP (class II-associated invariant chain peptide) molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and its gene contains 6 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DMB	NM_002118.5	c.*165C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000418107.3	NP_002109.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DMB	ENST00000418107.3	c.*165C>T		3_prime_UTR_variant	Exon 6 of 6	6	NM_002118.5	ENSP00000398890.2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19170 AN: 151930 Hom.: 1323 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.134 AC: 71685 AN: 535984 Hom.: 5481 Cov.: 7 AF XY: 0.135 AC XY: 38251 AN XY: 282374

African (AFR) AF: 0.0971 AC: 1366 AN: 14066

American (AMR) AF: 0.139 AC: 3066 AN: 22090

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 4454 AN: 14802

East Asian (EAS) AF: 0.0935 AC: 2986 AN: 31946

South Asian (SAS) AF: 0.172 AC: 8494 AN: 49254

European-Finnish (FIN) AF: 0.0969 AC: 3691 AN: 38088

Middle Eastern (MID) AF: 0.206 AC: 740 AN: 3592

European-Non Finnish (NFE) AF: 0.128 AC: 42544 AN: 332960

Other (OTH) AF: 0.149 AC: 4344 AN: 29186

GnomAD4 genome AF: 0.126 AC: 19168 AN: 152048 Hom.: 1323 Cov.: 31 AF XY: 0.126 AC XY: 9352 AN XY: 74318

African (AFR) AF: 0.101 AC: 4187 AN: 41458

American (AMR) AF: 0.156 AC: 2381 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3466

East Asian (EAS) AF: 0.0785 AC: 406 AN: 5174

South Asian (SAS) AF: 0.190 AC: 911 AN: 4806

European-Finnish (FIN) AF: 0.0970 AC: 1025 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8718 AN: 67992

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.129 Hom.: 4928

Bravo AF: 0.129

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.28
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: rs10751; hg19: chr6-32902583;