2-47801169-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000179.3(MSH6):c.3172+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,606,856 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 Likely benign (★★).
Frequency
Consequence
NM_000179.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 241796Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131904
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1454822Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 724032
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74258
ClinVar
Submissions by phenotype
Carcinoma of colon Uncertain:1
The MSH6 c.3172+14C>T variant was not identified in the literature nor was it identified in the ClinVar, Genesight-COGR, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, Insight Hereditary Tumors Database, databases. The variant was identified in dbSNP (ID: rs762990595) as N/A, database. The variant was identified in control databases in 5 of 268550 chromosomes at a frequency of 0.00002 (Genome Aggregation Consortium Feb 27, 2017) in the following populations: Latino in 3 of 34298 chromosomes (freq. 0.0001), European in 2 of 124606 chromosomes (freq. 0.00002). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Lynch syndrome 5 Benign:1
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Hereditary nonpolyposis colorectal neoplasms Benign:1
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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