4-144116874-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002099.8(GYPA):c.337G>A(p.Gly113Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000813 in 1,594,830 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002099.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYPA | NM_002099.8 | c.337G>A | p.Gly113Ser | missense_variant | 5/7 | ENST00000641688.3 | |
LOC105377460 | XR_002959803.2 | n.5270+1645C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYPA | ENST00000641688.3 | c.337G>A | p.Gly113Ser | missense_variant | 5/7 | NM_002099.8 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000889 AC: 135AN: 151934Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00119 AC: 299AN: 251010Hom.: 1 AF XY: 0.00121 AC XY: 164AN XY: 135640
GnomAD4 exome AF: 0.000805 AC: 1161AN: 1442780Hom.: 7 Cov.: 27 AF XY: 0.000880 AC XY: 633AN XY: 719190
GnomAD4 genome ? AF: 0.000888 AC: 135AN: 152050Hom.: 0 Cov.: 33 AF XY: 0.000996 AC XY: 74AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.337G>A (p.G113S) alteration is located in exon 5 (coding exon 5) of the GYPA gene. This alteration results from a G to A substitution at nucleotide position 337, causing the glycine (G) at amino acid position 113 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at