rs16970570

Variant names:

• chr17-77826765-G-A
• rs16970570
• ENST00000769794.1:n.418-21489C>T

Variant summary

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

The ENST00000769794.1(ENSG00000300182):​n.418-21489C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,952 control chromosomes in the GnomAD database, including 2,172 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 0.13 (2172 hom., cov: 32)
• Consequence: ENSG00000300182 ENST00000769794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 2 publications found

Genes affected

ENSG00000300182 (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 (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769794.1. 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
	ENSG00000300182	ENST00000769794.1		n.418-21489C>T		intron	N/A
	ENSG00000300182	ENST00000769795.1		n.122+13719C>T		intron	N/A
	ENSG00000300182	ENST00000769796.1		n.228+13392C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20418 AN: 151834 Hom.: 2165 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.135 AC: 20453 AN: 151952 Hom.: 2172 Cov.: 32 AF XY: 0.135 AC XY: 9997 AN XY: 74282

African (AFR) AF: 0.285 AC: 11801 AN: 41392

American (AMR) AF: 0.0790 AC: 1207 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1154 AN: 5142

South Asian (SAS) AF: 0.0946 AC: 456 AN: 4818

European-Finnish (FIN) AF: 0.0665 AC: 704 AN: 10592

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0658 AC: 4470 AN: 67956

Other (OTH) AF: 0.110 AC: 231 AN: 2106

Alfa AF: 0.0811 Hom.: 1442

Bravo AF: 0.144

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.49
PhyloP100		-2.1

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: rs16970570;

hg19: chr17-75822847;