14-23995055-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_198083.4(DHRS4L2):āc.330C>Gā(p.Ile110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,612,892 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198083.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHRS4L2 | NM_198083.4 | c.330C>G | p.Ile110Met | missense_variant | 3/8 | ENST00000335125.11 | NP_932349.2 | |
DHRS4L2 | NM_001193636.1 | c.27C>G | p.Ile9Met | missense_variant | 3/8 | NP_001180565.1 | ||
DHRS4L2 | NM_001193637.1 | c.27C>G | p.Ile9Met | missense_variant | 3/6 | NP_001180566.1 | ||
DHRS4L2 | NM_001193635.1 | c.222+4696C>G | intron_variant | NP_001180564.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 151668Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251360Hom.: 1 AF XY: 0.000199 AC XY: 27AN XY: 135842
GnomAD4 exome AF: 0.000104 AC: 152AN: 1461106Hom.: 5 Cov.: 31 AF XY: 0.000124 AC XY: 90AN XY: 726828
GnomAD4 genome AF: 0.000145 AC: 22AN: 151786Hom.: 1 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74138
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.330C>G (p.I110M) alteration is located in exon 3 (coding exon 3) of the DHRS4L2 gene. This alteration results from a C to G substitution at nucleotide position 330, causing the isoleucine (I) at amino acid position 110 to be replaced by a methionine (M). 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