rs1885373

Positions:

• chr9-35696805-C-T

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 0.925 in 152,260 control chromosomes in the GnomAD database, including 65,589 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 0.92 (65581 hom., cov: 32)
  • Exomes 𝑓: 1.0 (8 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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: 0.925 AC: 140713 AN: 152126 Hom.: 65535 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.949

GnomAD4 exome AF: 1.00 AC: 16 AN: 16 Hom.: 8 AF XY: 1.00 AC XY: 10 AN XY: 10

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.925 AC: 140819 AN: 152244 Hom.: 65581 Cov.: 32 AF XY: 0.926 AC XY: 68925 AN XY: 74434

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.949

Alfa AF: 0.970 Hom.: 70730

Bravo AF: 0.920

Asia WGS AF: 0.947 AC: 3296 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	0.039
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: rs1885373; hg19: chr9-35696802;