chr1-184702964-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_025191.4(EDEM3):c.2236C>T(p.Pro746Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.016 in 1,611,476 control chromosomes in the GnomAD database, including 255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_025191.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1757AN: 151984Hom.: 21 Cov.: 32
GnomAD3 exomes AF: 0.0118 AC: 2927AN: 248222Hom.: 26 AF XY: 0.0118 AC XY: 1582AN XY: 134242
GnomAD4 exome AF: 0.0165 AC: 24077AN: 1459374Hom.: 234 Cov.: 31 AF XY: 0.0162 AC XY: 11755AN XY: 726044
GnomAD4 genome AF: 0.0115 AC: 1756AN: 152102Hom.: 21 Cov.: 32 AF XY: 0.0115 AC XY: 858AN XY: 74348
ClinVar
Submissions by phenotype
Congenital disorder of glycosylation, type 2v Benign:1
European Non-Finnish population allele frequency is 1.620% (rs78444298, 2196/127710 alleles, 30 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.5.1, this variant is classified as BENIGN. Following criteria are met: BA1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at