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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904100	XR_007065977.1	n.79-3192G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302248	ENST00000785193.1	n.477-3192G>T		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs17779747; hg19: chr17-68494992;