7-76393850-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080744.2(SSC4D):c.1001C>T(p.Ala334Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,604,094 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.1001C>T | p.Ala334Val | missense_variant | Exon 8 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1088C>T | p.Ala363Val | missense_variant | Exon 9 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.494C>T | p.Ala165Val | missense_variant | Exon 5 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152212Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000699 AC: 16AN: 228744Hom.: 0 AF XY: 0.0000644 AC XY: 8AN XY: 124286
GnomAD4 exome AF: 0.000158 AC: 230AN: 1451882Hom.: 1 Cov.: 34 AF XY: 0.000140 AC XY: 101AN XY: 721356
GnomAD4 genome AF: 0.000112 AC: 17AN: 152212Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1001C>T (p.A334V) alteration is located in exon 8 (coding exon 7) of the SSC4D gene. This alteration results from a C to T substitution at nucleotide position 1001, causing the alanine (A) at amino acid position 334 to be replaced by a valine (V). 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