NM_001388490.1:c.38C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388490.1(MAP7D1):c.38C>T(p.Ala13Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,470,390 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_001388490.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP7D1 | NM_001388490.1 | c.38C>T | p.Ala13Val | missense_variant | Exon 1 of 17 | ENST00000474796.2 | NP_001375419.1 | |
MAP7D1 | NM_018067.5 | c.38C>T | p.Ala13Val | missense_variant | Exon 1 of 17 | NP_060537.3 | ||
MAP7D1 | NM_001286366.2 | c.38C>T | p.Ala13Val | missense_variant | Exon 1 of 18 | NP_001273295.1 | ||
MAP7D1 | NM_001286365.2 | c.38C>T | p.Ala13Val | missense_variant | Exon 1 of 16 | NP_001273294.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000209 AC: 14AN: 66878Hom.: 0 AF XY: 0.000179 AC XY: 7AN XY: 39122
GnomAD4 exome AF: 0.0000326 AC: 43AN: 1318270Hom.: 0 Cov.: 31 AF XY: 0.0000400 AC XY: 26AN XY: 649704
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.38C>T (p.A13V) alteration is located in exon 1 (coding exon 1) of the MAP7D1 gene. This alteration results from a C to T substitution at nucleotide position 38, causing the alanine (A) at amino acid position 13 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