rs907548

Variant names:

• chr3-89525702-C-T
• rs907548

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 0.205 in 151,950 control chromosomes in the GnomAD database, including 3,906 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 (3906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.205 AC: 31082 AN: 151830 Hom.: 3907 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.205 AC: 31091 AN: 151950 Hom.: 3906 Cov.: 32 AF XY: 0.206 AC XY: 15315 AN XY: 74256

African (AFR) AF: 0.0944 AC: 3917 AN: 41482

American (AMR) AF: 0.195 AC: 2960 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3464

East Asian (EAS) AF: 0.0878 AC: 454 AN: 5168

South Asian (SAS) AF: 0.0916 AC: 442 AN: 4826

European-Finnish (FIN) AF: 0.404 AC: 4264 AN: 10554

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18070 AN: 67926

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.240 Hom.: 2499

Bravo AF: 0.185

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.66
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs907548; hg19: chr3-89574852;