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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.583 AC: 24182 AN: 41482

American (AMR) AF: 0.672 AC: 10268 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2360 AN: 5170

South Asian (SAS) AF: 0.666 AC: 3210 AN: 4822

European-Finnish (FIN) AF: 0.748 AC: 7907 AN: 10566

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.686 AC: 46634 AN: 67986

Other (OTH) AF: 0.666 AC: 1408 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.64
PhyloP100		-0.57
PromoterAI		-0.0065	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1342024; hg19: chr9-75695660;