rs1361925

Positions:

• chr9-30085412-T-C
• chr9-30085412-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 0.607 in 151,876 control chromosomes in the GnomAD database, including 28,269 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 0.61 (28269 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.607 AC: 92101 AN: 151760 Hom.: 28252 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.607 AC: 92156 AN: 151876 Hom.: 28269 Cov.: 31 AF XY: 0.603 AC XY: 44805 AN XY: 74248

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.623

Alfa AF: 0.603 Hom.: 15113

Bravo AF: 0.614

Asia WGS AF: 0.422 AC: 1464 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361925; hg19: chr9-30085410;