rs11556218
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_172217.5(IL16):āc.3441T>Gā(p.Asn1147Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 1,613,540 control chromosomes in the GnomAD database, including 8,302 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_172217.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL16 | NM_172217.5 | c.3441T>G | p.Asn1147Lys | missense_variant | 17/19 | ENST00000683961.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL16 | ENST00000683961.1 | c.3441T>G | p.Asn1147Lys | missense_variant | 17/19 | NM_172217.5 | A2 | ||
ENST00000607019.1 | n.62-2299A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17779AN: 152166Hom.: 1334 Cov.: 33
GnomAD3 exomes AF: 0.0964 AC: 24215AN: 251204Hom.: 1503 AF XY: 0.0894 AC XY: 12138AN XY: 135774
GnomAD4 exome AF: 0.0909 AC: 132794AN: 1461256Hom.: 6965 Cov.: 32 AF XY: 0.0887 AC XY: 64490AN XY: 726976
GnomAD4 genome ? AF: 0.117 AC: 17799AN: 152284Hom.: 1337 Cov.: 33 AF XY: 0.112 AC XY: 8372AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at