rs16857178

Positions:

• chr2-11117379-G-A

Variant summary

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

The NR_040080.1(FLJ33534):​n.984+3384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,194 control chromosomes in the GnomAD database, including 3,136 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 0.13 (3136 hom., cov: 33)
• Consequence: FLJ33534 NR_040080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

Genes affected

ENSG00000145063 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLJ33534	NR_040080.1	n.984+3384C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000145063	ENST00000536743.5	n.984+3384C>T		intron_variant		5
ENSG00000145063	ENST00000544306.5	n.793+3384C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19296 AN: 152076 Hom.: 3124 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.127 AC: 19336 AN: 152194 Hom.: 3136 Cov.: 33 AF XY: 0.124 AC XY: 9224 AN XY: 74398

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0500 Hom.: 796

Bravo AF: 0.140

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16857178; hg19: chr2-11257505;