NM_003873.7:c.2571C>G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003873.7(NRP1):āc.2571C>Gā(p.Ile857Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000351 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_003873.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251406Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135866
GnomAD4 exome AF: 0.000372 AC: 544AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.000352 AC XY: 256AN XY: 727232
GnomAD4 genome AF: 0.000145 AC: 22AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74302
ClinVar
Submissions by phenotype
NRP1-related disorder Uncertain:1
The NRP1 c.2571C>G variant is predicted to result in the amino acid substitution p.Ile857Met. This variant has been reported in the heterozygous state in an individual with Kallmann syndrome; however, the variant was also detected in the unaffected mother (Marcos et al. 2017. PubMed ID: 28334861). This variant is reported in 0.034% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at