rs9909466

Variant names:

• chr17-80525440-G-C
• rs9909466
• ENST00000776907.1:n.684+2648C>G

Your query was ambiguous. Multiple possible variants found:

• chr17-80525440-G-C
• chr17-80525440-G-T

Variant summary

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

The ENST00000776907.1(ENSG00000301193):​n.684+2648C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,162 control chromosomes in the GnomAD database, including 2,619 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 0.18 (2619 hom., cov: 32)
• Consequence: ENSG00000301193 ENST00000776907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 3 publications found

Genes affected

ENSG00000301193 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301193	ENST00000776907.1	n.684+2648C>G		intron_variant	Intron 1 of 3
ENSG00000301193	ENST00000776908.1	n.612+2648C>G		intron_variant	Intron 1 of 2
ENSG00000301193	ENST00000776909.1	n.562+2648C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27293 AN: 152044 Hom.: 2619 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.179 AC: 27299 AN: 152162 Hom.: 2619 Cov.: 32 AF XY: 0.174 AC XY: 12942 AN XY: 74390

African (AFR) AF: 0.167 AC: 6952 AN: 41528

American (AMR) AF: 0.150 AC: 2294 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3470

East Asian (EAS) AF: 0.0316 AC: 163 AN: 5164

South Asian (SAS) AF: 0.107 AC: 517 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10594

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14248 AN: 67966

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.0938 Hom.: 161

Bravo AF: 0.177

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs9909466; hg19: chr17-78499240;