rs9326050

chr1-40256236-T-Cchr1-40256236-T-G

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 0.562 in 152,036 control chromosomes in the GnomAD database, including 25,189 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 0.56 (25189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85406 AN: 151918 Hom.: 25147 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.562 AC: 85512 AN: 152036 Hom.: 25189 Cov.: 31 AF XY: 0.568 AC XY: 42244 AN XY: 74312

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.516

Alfa AF: 0.521 Hom.: 3491

Bravo AF: 0.567

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.72
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9326050; hg19: chr1-40721908; COSMIC: COSV65638917;