rs9826507

chr3-137072544-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.364 in 152,144 control chromosomes in the GnomAD database, including 10,351 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 0.36 (10351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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: 0.364 AC: 55308 AN: 152026 Hom.: 10349 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.364 AC: 55328 AN: 152144 Hom.: 10351 Cov.: 33 AF XY: 0.358 AC XY: 26663 AN XY: 74374

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.404

Alfa AF: 0.362 Hom.: 1278

Bravo AF: 0.363

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
Cadd	Benign	19
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9826507; hg19: chr3-136791386;