rs7204454

Variant names:

• chr16-82625589-G-C
• rs7204454
• ENST00000793365.1:n.1013+708C>G

Variant summary

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

The ENST00000793365.1(ENSG00000303284):​n.1013+708C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,130 control chromosomes in the GnomAD database, including 26,674 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 0.58 (26674 hom., cov: 34)
• Consequence: ENSG00000303284 ENST00000793365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 8 publications found

Genes affected

ENSG00000303284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 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
ENSG00000303284	ENST00000793365.1	n.1013+708C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88890 AN: 152012 Hom.: 26655 Cov.: 34

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.585 AC: 88939 AN: 152130 Hom.: 26674 Cov.: 34 AF XY: 0.584 AC XY: 43433 AN XY: 74366

African (AFR) AF: 0.512 AC: 21235 AN: 41496

American (AMR) AF: 0.466 AC: 7119 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1925 AN: 5176

South Asian (SAS) AF: 0.608 AC: 2930 AN: 4818

European-Finnish (FIN) AF: 0.701 AC: 7418 AN: 10582

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44504 AN: 67982

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.621 Hom.: 3685

Bravo AF: 0.558

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.43
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs7204454; hg19: chr16-82659194;