rs17779747

Variant names:

• chr17-70498851-G-T
• rs17779747
• ENST00000785193.1:n.477-3192G>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000785193.1(ENSG00000302248):​n.477-3192G>T variant causes a intron change. The variant allele was found at a frequency of 0.24 in 151,988 control chromosomes in the GnomAD database, including 5,329 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 0.24 (5329 hom., cov: 32)
• Consequence: ENSG00000302248 ENST00000785193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.95
• Publications: 50 publications found

Genes affected

ENSG00000302248 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785193.1. 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
	ENSG00000302248	ENST00000785193.1		n.477-3192G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36393 AN: 151870 Hom.: 5316 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36423 AN: 151988 Hom.: 5329 Cov.: 32 AF XY: 0.235 AC XY: 17498 AN XY: 74304

African (AFR) AF: 0.0904 AC: 3753 AN: 41494

American (AMR) AF: 0.256 AC: 3902 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3466

East Asian (EAS) AF: 0.0761 AC: 394 AN: 5178

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2577 AN: 10562

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22361 AN: 67900

Other (OTH) AF: 0.275 AC: 577 AN: 2102

Alfa AF: 0.296 Hom.: 26236

Bravo AF: 0.232

Asia WGS AF: 0.210 AC: 729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	19
DANN	Benign	0.63
PhyloP100		3.9

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: rs17779747;

hg19: chr17-68494992;