16-9560199-C-T

Variant names:

• chr16-9560199-C-T
• rs1074042
• ENST00000634367.2:n.214+1122C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188388.1(LOC132205950):​n.283+1122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,108 control chromosomes in the GnomAD database, including 20,388 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20388 hom., cov: 33)
• Consequence: LOC132205950 NR_188388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

ENSG00000283003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC132205950	NR_188388.1	n.283+1122C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283003	ENST00000634367.2	n.214+1122C>T		intron_variant	Intron 2 of 4	5
ENSG00000283003	ENST00000653393.2	n.289+1122C>T		intron_variant	Intron 2 of 5
ENSG00000283003	ENST00000701200.1	n.215+1122C>T		intron_variant	Intron 2 of 4
ENSG00000283003	ENST00000701702.1	n.283+1122C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77625 AN: 151992 Hom.: 20360 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77716 AN: 152108 Hom.: 20388 Cov.: 33 AF XY: 0.506 AC XY: 37631 AN XY: 74340

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.527

Alfa AF: 0.504 Hom.: 40038

Bravo AF: 0.538

Asia WGS AF: 0.626 AC: 2175 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1074042; hg19: chr16-9654056;