rs4742323

Variant names:

• chr9-7286743-C-G
• rs4742323

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 0.389 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.301 AC: 12463 AN: 41452

American (AMR) AF: 0.396 AC: 6048 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1149 AN: 3464

East Asian (EAS) AF: 0.811 AC: 4201 AN: 5178

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4826

European-Finnish (FIN) AF: 0.483 AC: 5084 AN: 10530

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26562 AN: 67964

Other (OTH) AF: 0.399 AC: 842 AN: 2110

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
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs4742323; hg19: chr9-7286743;