chr16-9569798-C-T

Position:

• chr16-9569798-C-T

Variant summary

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

The NR_188388.1(LOC132205950):​n.643+3208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,928 control chromosomes in the GnomAD database, including 12,159 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 0.39 (12159 hom., cov: 32)
• Consequence: LOC132205950 NR_188388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

Genes affected

ENSG00000283003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC132205950	NR_188388.1	n.643+3208C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283003	ENST00000634367.2	n.574+3208C>T		intron_variant		5
ENSG00000283003	ENST00000653393.2	n.649+3208C>T		intron_variant
ENSG00000283003	ENST00000701200.1	n.575+3208C>T		intron_variant
ENSG00000283003	ENST00000701702.1	n.1052+2799C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59631 AN: 151810 Hom.: 12153 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.393 AC: 59655 AN: 151928 Hom.: 12159 Cov.: 32 AF XY: 0.392 AC XY: 29111 AN XY: 74248

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.407

Alfa AF: 0.428 Hom.: 8505

Bravo AF: 0.392

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468769; hg19: chr16-9663655;