rs17724552

Variant names:

• chr9-107238073-G-A
• rs17724552
• ENST00000807600.1:n.97+11068C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-107238073-G-A
• chr9-107238073-G-T

Variant summary

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

The ENST00000807600.1(ENSG00000304997):​n.97+11068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0983 in 152,112 control chromosomes in the GnomAD database, including 869 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 0.098 (869 hom., cov: 33)
• Consequence: ENSG00000304997 ENST00000807600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679
• Publications: 4 publications found

Genes affected

ENSG00000304997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 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
ENSG00000304997	ENST00000807600.1	n.97+11068C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14936 AN: 151994 Hom.: 868 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.0912

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0983 AC: 14951 AN: 152112 Hom.: 869 Cov.: 33 AF XY: 0.0971 AC XY: 7220 AN XY: 74342

African (AFR) AF: 0.0562 AC: 2334 AN: 41506

American (AMR) AF: 0.0910 AC: 1390 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5174

South Asian (SAS) AF: 0.163 AC: 787 AN: 4816

European-Finnish (FIN) AF: 0.0713 AC: 753 AN: 10568

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8690 AN: 67980

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.120 Hom.: 2166

Bravo AF: 0.0963

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.49
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs17724552; hg19: chr9-110000354;