chr1-145960561-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001039888.4(ANKRD34A):c.1199G>A(p.Ser400Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000213 in 1,584,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039888.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD34A | ENST00000606888.3 | c.1199G>A | p.Ser400Asn | missense_variant | Exon 4 of 4 | 2 | NM_001039888.4 | ENSP00000475189.1 | ||
ENSG00000280778 | ENST00000625258.1 | c.-29-16523C>T | intron_variant | Intron 1 of 3 | 5 | ENSP00000487094.1 | ||||
ENSG00000280778 | ENST00000630636.1 | n.713+1457C>T | intron_variant | Intron 3 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000890 AC: 18AN: 202190Hom.: 0 AF XY: 0.000101 AC XY: 11AN XY: 109130
GnomAD4 exome AF: 0.000216 AC: 310AN: 1432164Hom.: 0 Cov.: 33 AF XY: 0.000220 AC XY: 156AN XY: 709426
GnomAD4 genome AF: 0.000184 AC: 28AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1199G>A (p.S400N) alteration is located in exon 4 (coding exon 1) of the ANKRD34A gene. This alteration results from a G to A substitution at nucleotide position 1199, causing the serine (S) at amino acid position 400 to be replaced by an asparagine (N). 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