chr19-38410968-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_170604.3(RASGRP4):c.1883C>T(p.Ser628Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000874 in 1,602,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_170604.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASGRP4 | ENST00000615439.5 | c.1883C>T | p.Ser628Phe | missense_variant | Exon 16 of 17 | 1 | NM_170604.3 | ENSP00000479844.1 | ||
RASGRP4 | ENST00000587738.2 | c.1883C>T | p.Ser628Phe | missense_variant | Exon 16 of 17 | 5 | ENSP00000465772.1 | |||
RASGRP4 | ENST00000586305.5 | c.1841C>T | p.Ser614Phe | missense_variant | Exon 16 of 17 | 1 | ENSP00000467604.1 | |||
RASGRP4 | ENST00000454404.6 | c.1781C>T | p.Ser594Phe | missense_variant | Exon 16 of 17 | 1 | ENSP00000416463.2 | |||
RASGRP4 | ENST00000587753.5 | c.1676C>T | p.Ser559Phe | missense_variant | Exon 16 of 17 | 1 | ENSP00000468483.1 | |||
RASGRP4 | ENST00000614135.4 | c.1607C>T | p.Ser536Phe | missense_variant | Exon 15 of 16 | 5 | ENSP00000479078.1 | |||
RASGRP4 | ENST00000617966.4 | c.1592C>T | p.Ser531Phe | missense_variant | Exon 14 of 15 | 5 | ENSP00000479888.1 | |||
RASGRP4 | ENST00000622174.4 | c.1316C>T | p.Ser439Phe | missense_variant | Exon 13 of 14 | 5 | ENSP00000484345.1 | |||
RASGRP4 | ENST00000589358.5 | n.1883C>T | non_coding_transcript_exon_variant | Exon 16 of 18 | 5 | ENSP00000465742.1 | ||||
RASGRP4 | ENST00000589474.5 | n.1841C>T | non_coding_transcript_exon_variant | Exon 16 of 18 | 5 | ENSP00000466928.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000309 AC: 7AN: 226382Hom.: 0 AF XY: 0.0000408 AC XY: 5AN XY: 122448
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1449928Hom.: 0 Cov.: 31 AF XY: 0.00000972 AC XY: 7AN XY: 720036
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1883C>T (p.S628F) alteration is located in exon 16 (coding exon 16) of the RASGRP4 gene. This alteration results from a C to T substitution at nucleotide position 1883, causing the serine (S) at amino acid position 628 to be replaced by a phenylalanine (F). 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