rs1162608

Variant names:

• chr9-24605823-A-G
• rs1162608

Your query was ambiguous. Multiple possible variants found:

• chr9-24605823-A-G
• chr9-24605823-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.214 in 151,784 control chromosomes in the GnomAD database, including 3,872 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 0.21 (3872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32516 AN: 151666 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.214 AC: 32522 AN: 151784 Hom.: 3872 Cov.: 32 AF XY: 0.212 AC XY: 15768 AN XY: 74216

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.256

Alfa AF: 0.268 Hom.: 7072

Bravo AF: 0.214

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1162608; hg19: chr9-24605821;