rs148359873

chr9-31450668-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0118 in 151,968 control chromosomes in the GnomAD database, including 25 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 0.012 (25 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0118 (1800/151968) while in subpopulation SAS AF= 0.0316 (152/4804). AF 95% confidence interval is 0.0275. There are 25 homozygotes in gnomad4. There are 931 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 25 gene

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: 0.0119 AC: 1804 AN: 151850 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00259

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00755

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0118 AC: 1800 AN: 151968 Hom.: 25 Cov.: 32 AF XY: 0.0125 AC XY: 931 AN XY: 74270

Gnomad4 AFR AF: 0.00258

Gnomad4 AMR AF: 0.00754

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0316

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0134 Hom.: 2

Bravo AF: 0.00965

Asia WGS AF: 0.00925 AC: 32 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.34
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs148359873; hg19: chr9-31450666;