rs935885

Variant names:

• chr15-44718817-C-A
• rs935885
• ENST00000561424.5:n.*172C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-44718817-C-A
• chr15-44718817-C-G
• chr15-44718817-C-T

Variant summary

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

The ENST00000561424.5(B2M):​n.*172C>A 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 0.942 in 152,280 control chromosomes in the GnomAD database, including 67,628 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 0.94 (67627 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: B2M ENST00000561424.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

B2M (HGNC:914): (beta-2-microglobulin) This gene encodes a serum protein found in association with the major histocompatibility complex (MHC) class I heavy chain on the surface of nearly all nucleated cells. The protein has a predominantly beta-pleated sheet structure that can form amyloid fibrils in some pathological conditions. The encoded antimicrobial protein displays antibacterial activity in amniotic fluid. A mutation in this gene has been shown to result in hypercatabolic hypoproteinemia.[provided by RefSeq, Aug 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 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
B2M	ENST00000561424.5	n.*172C>A		non_coding_transcript_exon_variant	Exon 5 of 5	3		ENSP00000453191.1
B2M	ENST00000561424.5	n.*172C>A		3_prime_UTR_variant	Exon 5 of 5	3		ENSP00000453191.1

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143271 AN: 152160 Hom.: 67581 Cov.: 31

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.936

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.942 AC: 143376 AN: 152278 Hom.: 67627 Cov.: 31 AF XY: 0.939 AC XY: 69912 AN XY: 74442

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.936

Alfa AF: 0.949 Hom.: 13905

Bravo AF: 0.935

Asia WGS AF: 0.860 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs935885; hg19: chr15-45011015;