ENST00000826416.1:n.198+19377C>G

Variant names:

• chr17-16913229-C-G
• rs4792793
• ENST00000826416.1:n.198+19377C>G

Variant summary

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

The ENST00000826416.1(ENSG00000307457):​n.198+19377C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,130 control chromosomes in the GnomAD database, including 3,084 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 0.20 (3084 hom., cov: 32)
• Consequence: ENSG00000307457 ENST00000826416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 1 publications found

Genes affected

ENSG00000307457 (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 (SAS) allele frequency at 95% confidence interval = 0.25 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
ENSG00000307457	ENST00000826416.1	n.198+19377C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29878 AN: 152012 Hom.: 3082 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.197 AC: 29914 AN: 152130 Hom.: 3084 Cov.: 32 AF XY: 0.198 AC XY: 14751 AN XY: 74364

African (AFR) AF: 0.245 AC: 10147 AN: 41480

American (AMR) AF: 0.178 AC: 2722 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5184

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1918 AN: 10574

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11327 AN: 68002

Other (OTH) AF: 0.167 AC: 353 AN: 2114

Alfa AF: 0.0704 Hom.: 92

Bravo AF: 0.198

Asia WGS AF: 0.284 AC: 987 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	0.48
DANN	Benign	0.35
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4792793; hg19: chr17-16816543; COSMIC: COSV60076595;