rs1342024

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;