rs717119

Variant names:

• chr17-70468777-A-G
• rs717119
• ENST00000785193.1:n.476+28998A>G

Variant summary

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

The ENST00000785193.1(ENSG00000302248):​n.476+28998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,162 control chromosomes in the GnomAD database, including 3,471 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 0.19 (3471 hom., cov: 32)
• Consequence: ENSG00000302248 ENST00000785193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 1 publications found

Genes affected

ENSG00000302248 (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 = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904100	XR_007065977.1	n.78+28998A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302248	ENST00000785193.1	n.476+28998A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29286 AN: 152042 Hom.: 3470 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.192 AC: 29283 AN: 152162 Hom.: 3471 Cov.: 32 AF XY: 0.196 AC XY: 14616 AN XY: 74388

African (AFR) AF: 0.121 AC: 5037 AN: 41536

American (AMR) AF: 0.269 AC: 4107 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3468

East Asian (EAS) AF: 0.579 AC: 2992 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1643 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1082 AN: 10600

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12941 AN: 67976

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.190 Hom.: 366

Bravo AF: 0.212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.36
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs717119; hg19: chr17-68464918; COSMIC: COSV50866177;