8-27921823-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_173833.6(SCARA5):c.664G>T(p.Asp222Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,547,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173833.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARA5 | NM_173833.6 | c.664G>T | p.Asp222Tyr | missense_variant | Exon 4 of 9 | ENST00000354914.8 | NP_776194.2 | |
SCARA5 | NM_001413201.1 | c.535G>T | p.Asp179Tyr | missense_variant | Exon 3 of 8 | NP_001400130.1 | ||
SCARA5 | NM_001413202.1 | c.664G>T | p.Asp222Tyr | missense_variant | Exon 4 of 7 | NP_001400131.1 | ||
SCARA5 | NM_001413203.1 | c.-141G>T | 5_prime_UTR_variant | Exon 3 of 8 | NP_001400132.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCARA5 | ENST00000354914.8 | c.664G>T | p.Asp222Tyr | missense_variant | Exon 4 of 9 | 2 | NM_173833.6 | ENSP00000346990.3 | ||
SCARA5 | ENST00000524352.5 | c.664G>T | p.Asp222Tyr | missense_variant | Exon 4 of 7 | 1 | ENSP00000428663.1 | |||
SCARA5 | ENST00000518030.1 | c.535G>T | p.Asp179Tyr | missense_variant | Exon 2 of 5 | 1 | ENSP00000430713.1 | |||
SCARA5 | ENST00000380385.6 | c.242-12080G>T | intron_variant | Intron 3 of 7 | 1 | ENSP00000369746.2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000686 AC: 1AN: 145816Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80048
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1395132Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 689560
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.664G>T (p.D222Y) alteration is located in exon 4 (coding exon 3) of the SCARA5 gene. This alteration results from a G to T substitution at nucleotide position 664, causing the aspartic acid (D) at amino acid position 222 to be replaced by a tyrosine (Y). 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