rs7661933
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002100.6(GYPB):c.175+84T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 727,816 control chromosomes in the GnomAD database, including 34,824 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 0.27 ( 6550 hom., cov: 32)
Exomes 𝑓: 0.30 ( 28274 hom. )
Consequence
GYPB
NM_002100.6 intron
NM_002100.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.83
Genes affected
GYPB (HGNC:4703): (glycophorin B (MNS blood group)) Glycophorins A (GYPA) and B (GYPB) are major sialoglycoproteins of the human erythrocyte membrane which bear the antigenic determinants for the MN and Ss blood groups. GYPB gene consists of 5 exons and has 97% sequence homology with GYPA from the 5' UTR to the coding sequence encoding the first 45 amino acids. In addition to the M or N and S or s antigens, that commonly occur in all populations, about 40 related variant phenotypes have been identified. These variants include all the variants of the Miltenberger complex and several isoforms of Sta; also, Dantu, Sat, He, Mg, and deletion variants Ena, S-s-U- and Mk. Most of the variants are the result of gene recombinations between GYPA and GYPB. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYPB | NM_002100.6 | c.175+84T>A | intron_variant | ENST00000502664.6 | |||
GYPB | NM_001304382.1 | c.97+84T>A | intron_variant | ||||
GYPB | XM_011531903.3 | c.175+84T>A | intron_variant | ||||
GYPB | XM_011531904.4 | c.148+84T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYPB | ENST00000502664.6 | c.175+84T>A | intron_variant | 1 | NM_002100.6 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41439AN: 151364Hom.: 6543 Cov.: 32
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GnomAD4 exome AF: 0.301 AC: 173306AN: 576336Hom.: 28274 Cov.: 7 AF XY: 0.305 AC XY: 94846AN XY: 311208
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GnomAD4 genome ? AF: 0.274 AC: 41464AN: 151480Hom.: 6550 Cov.: 32 AF XY: 0.276 AC XY: 20407AN XY: 74060
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at