chr3-153149499-C-A

Variant names:

• chr3-153149499-C-A
• rs9830448

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 0.257 in 152,084 control chromosomes in the GnomAD database, including 6,202 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 0.26 (6202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39051 AN: 151964 Hom.: 6204 Cov.: 32

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.257 AC: 39052 AN: 152084 Hom.: 6202 Cov.: 32 AF XY: 0.256 AC XY: 19045 AN XY: 74320

African (AFR) AF: 0.0728 AC: 3025 AN: 41540

American (AMR) AF: 0.323 AC: 4929 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.148 AC: 761 AN: 5156

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3097 AN: 10554

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23947 AN: 67956

Other (OTH) AF: 0.278 AC: 585 AN: 2106

Alfa AF: 0.325 Hom.: 27250

Bravo AF: 0.252

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9830448; hg19: chr3-152867288;