rs9285673

Variant names:

• chr5-148793365-A-C
• rs9285673

Your query was ambiguous. Multiple possible variants found:

• chr5-148793365-A-C
• chr5-148793365-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.197 in 152,152 control chromosomes in the GnomAD database, including 5,106 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 0.20 (5106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.196 AC: 29856 AN: 152034 Hom.: 5085 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.197 AC: 29923 AN: 152152 Hom.: 5106 Cov.: 32 AF XY: 0.194 AC XY: 14424 AN XY: 74394

African (AFR) AF: 0.463 AC: 19201 AN: 41444

American (AMR) AF: 0.0984 AC: 1504 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.0609 AC: 316 AN: 5190

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1592 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0941 AC: 6401 AN: 68006

Other (OTH) AF: 0.157 AC: 333 AN: 2116

Alfa AF: 0.114 Hom.: 3289

Bravo AF: 0.205

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.48
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9285673; hg19: chr5-148172928;