rs3045983
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The NM_002439.5(MSH3):c.199_207delCCAGCTCCC(p.Pro67_Pro69del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,521,560 control chromosomes in the GnomAD database, including 63,065 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002439.5 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSH3 | NM_002439.5 | c.199_207delCCAGCTCCC | p.Pro67_Pro69del | conservative_inframe_deletion | Exon 1 of 24 | ENST00000265081.7 | NP_002430.3 | |
DHFR | NM_000791.4 | c.-442_-434delAGCTGGGGG | 5_prime_UTR_variant | Exon 1 of 6 | ENST00000439211.7 | NP_000782.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH3 | ENST00000265081.7 | c.199_207delCCAGCTCCC | p.Pro67_Pro69del | conservative_inframe_deletion | Exon 1 of 24 | 1 | NM_002439.5 | ENSP00000265081.6 | ||
MSH3 | ENST00000667069.1 | c.199_207delCCAGCTCCC | p.Pro67_Pro69del | conservative_inframe_deletion | Exon 1 of 22 | ENSP00000499502.1 | ||||
DHFR | ENST00000439211.7 | c.-442_-434delAGCTGGGGG | 5_prime_UTR_variant | Exon 1 of 6 | 1 | NM_000791.4 | ENSP00000396308.2 | |||
MSH3 | ENST00000670357.1 | n.199_207delCCAGCTCCC | non_coding_transcript_exon_variant | Exon 1 of 25 | ENSP00000499791.1 |
Frequencies
GnomAD3 genomes AF: 0.258 AC: 38926AN: 150902Hom.: 5181 Cov.: 0
GnomAD3 exomes AF: 0.309 AC: 39028AN: 126454Hom.: 7452 AF XY: 0.318 AC XY: 22606AN XY: 71060
GnomAD4 exome AF: 0.272 AC: 373255AN: 1370550Hom.: 57880 AF XY: 0.276 AC XY: 187394AN XY: 678858
GnomAD4 genome AF: 0.258 AC: 38939AN: 151010Hom.: 5185 Cov.: 0 AF XY: 0.256 AC XY: 18875AN XY: 73796
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is associated with the following publications: (PMID: 25927356) -
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not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -
Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at