rs1342024

Variant names:

• chr9-73080744-C-G
• rs1342024

Your query was ambiguous. Multiple possible variants found:

• chr9-73080744-C-G
• chr9-73080744-C-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 0.651 in 152,098 control chromosomes in the GnomAD database, including 32,505 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 0.65 (32505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 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: 0.651 AC: 98879 AN: 151980 Hom.: 32471 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.651 AC: 98970 AN: 152098 Hom.: 32505 Cov.: 32 AF XY: 0.653 AC XY: 48593 AN XY: 74362

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.666

Alfa AF: 0.563 Hom.: 1601

Bravo AF: 0.640

Asia WGS AF: 0.572 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342024; hg19: chr9-75695660;