17-16916595-A-G

Variant names:

• chr17-16916595-A-G
• rs11654076
• ENST00000826416.1:n.199-19678A>G

Variant summary

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

The ENST00000826416.1(ENSG00000307457):​n.199-19678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,986 control chromosomes in the GnomAD database, including 8,080 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 0.31 (8080 hom., cov: 32)
• Consequence: ENSG00000307457 ENST00000826416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826416.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307457	ENST00000826416.1		n.199-19678A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47412 AN: 151866 Hom.: 8081 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.312 AC: 47444 AN: 151986 Hom.: 8080 Cov.: 32 AF XY: 0.314 AC XY: 23305 AN XY: 74262

African (AFR) AF: 0.163 AC: 6770 AN: 41486

American (AMR) AF: 0.343 AC: 5247 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1088 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5158

South Asian (SAS) AF: 0.407 AC: 1954 AN: 4796

European-Finnish (FIN) AF: 0.370 AC: 3901 AN: 10532

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25967 AN: 67954

Other (OTH) AF: 0.354 AC: 746 AN: 2108

Alfa AF: 0.291 Hom.: 3710

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11654076; hg19: chr17-16819909;