rs1416483

Variant names:

• chr6-150407426-G-C
• rs1416483
• ENST00000743816.1:n.*167C>G

Variant summary

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

The ENST00000743816.1(ENSG00000296954):​n.*167C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,120 control chromosomes in the GnomAD database, including 4,355 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 0.22 (4355 hom., cov: 32)
• Consequence: ENSG00000296954 ENST00000743816.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 publications found

Genes affected

ENSG00000296954 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296954	ENST00000743816.1	n.*167C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33826 AN: 152002 Hom.: 4352 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.223 AC: 33848 AN: 152120 Hom.: 4355 Cov.: 32 AF XY: 0.227 AC XY: 16874 AN XY: 74376

African (AFR) AF: 0.211 AC: 8750 AN: 41504

American (AMR) AF: 0.285 AC: 4353 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2969 AN: 5152

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4814

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10584

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12667 AN: 67988

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.204 Hom.: 425

Bravo AF: 0.231

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.66
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs1416483; hg19: chr6-150728562;