NM_153704.6:c.*19T>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_153704.6(TMEM67):c.*19T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,442,244 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_153704.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2450AN: 152122Hom.: 71 Cov.: 33
GnomAD3 exomes AF: 0.00418 AC: 1029AN: 246124Hom.: 23 AF XY: 0.00337 AC XY: 449AN XY: 133350
GnomAD4 exome AF: 0.00167 AC: 2148AN: 1290004Hom.: 45 Cov.: 18 AF XY: 0.00143 AC XY: 931AN XY: 650488
GnomAD4 genome AF: 0.0162 AC: 2465AN: 152240Hom.: 71 Cov.: 33 AF XY: 0.0158 AC XY: 1176AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:2
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Meckel syndrome, type 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not specified Benign:1
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Nephronophthisis 11 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Joubert syndrome 6 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at