17-70320318-C-T

Variant names:

• chr17-70320318-C-T
• rs16975551
• ENST00000592809.1:n.177-6930G>A

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.177-6930G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,114 control chromosomes in the GnomAD database, including 1,300 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 0.12 (1300 hom., cov: 32)
• Consequence: ENSG00000267109 ENST00000592809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 10 publications found

Genes affected

ENSG00000267109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592809.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267109	ENST00000592809.1	TSL:3	n.177-6930G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17559 AN: 151994 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.115 AC: 17565 AN: 152114 Hom.: 1300 Cov.: 32 AF XY: 0.116 AC XY: 8589 AN XY: 74328

African (AFR) AF: 0.0324 AC: 1344 AN: 41534

American (AMR) AF: 0.152 AC: 2317 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3470

East Asian (EAS) AF: 0.164 AC: 847 AN: 5162

South Asian (SAS) AF: 0.141 AC: 676 AN: 4810

European-Finnish (FIN) AF: 0.0914 AC: 964 AN: 10544

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10158 AN: 68000

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.116 Hom.: 493

Bravo AF: 0.115

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16975551;

hg19: chr17-68316459;