rs16857178

Variant names:

• chr2-11117379-G-A
• rs16857178
• ENST00000536743.5:n.984+3384C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536743.5(ENSG00000145063):​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: ENSG00000145063 ENST00000536743.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 8 publications found

Genes affected

ENSG00000145063 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FLJ33534	NR_040080.1	n.984+3384C>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000145063	ENST00000536743.5	n.984+3384C>T		intron_variant	Intron 6 of 7	5
ENSG00000145063	ENST00000544306.5	n.793+3384C>T		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.382 AC: 15870 AN: 41504

American (AMR) AF: 0.0519 AC: 793 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.0156 AC: 81 AN: 5182

South Asian (SAS) AF: 0.0635 AC: 306 AN: 4820

European-Finnish (FIN) AF: 0.0337 AC: 357 AN: 10594

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0233 AC: 1586 AN: 68028

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0662 Hom.: 3547

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
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16857178; hg19: chr2-11257505;