rs17468071

Variant names:

• chr9-23679838-T-C
• rs17468071

Your query was ambiguous. Multiple possible variants found:

• chr9-23679838-T-C
• chr9-23679838-T-G

Variant summary

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

The variant allele was found at a frequency of 0.0924 in 152,154 control chromosomes in the GnomAD database, including 732 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 0.092 (732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14052 AN: 152036 Hom.: 731 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0924 AC: 14060 AN: 152154 Hom.: 732 Cov.: 32 AF XY: 0.0900 AC XY: 6697 AN XY: 74370

African (AFR) AF: 0.0961 AC: 3990 AN: 41500

American (AMR) AF: 0.0650 AC: 993 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0260 AC: 125 AN: 4816

European-Finnish (FIN) AF: 0.0903 AC: 957 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7498 AN: 68002

Other (OTH) AF: 0.0860 AC: 182 AN: 2116

Alfa AF: 0.0971 Hom.: 1642

Bravo AF: 0.0924

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.68
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs17468071; hg19: chr9-23679836;