rs4742323

Variant names:

• chr9-7286743-C-G
• rs4742323

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 0.389 in 151,994 control chromosomes in the GnomAD database, including 12,409 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 0.39 (12409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.389 AC: 59142 AN: 151876 Hom.: 12403 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.389 AC: 59178 AN: 151994 Hom.: 12409 Cov.: 32 AF XY: 0.397 AC XY: 29462 AN XY: 74300

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.399

Alfa AF: 0.388 Hom.: 1445

Bravo AF: 0.379

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4742323; hg19: chr9-7286743;