rs9826507

Variant names:

• chr3-137072544-G-A
• rs9826507

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;