rs1078248

Variant names:

• chr3-43752865-C-T
• rs1078248

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 0.277 in 151,972 control chromosomes in the GnomAD database, including 6,050 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 0.28 (6050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42030 AN: 151850 Hom.: 6046 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.277 AC: 42061 AN: 151972 Hom.: 6050 Cov.: 32 AF XY: 0.272 AC XY: 20247 AN XY: 74314

African (AFR) AF: 0.318 AC: 13170 AN: 41462

American (AMR) AF: 0.215 AC: 3277 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3464

East Asian (EAS) AF: 0.157 AC: 812 AN: 5170

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2492 AN: 10588

Middle Eastern (MID) AF: 0.329 AC: 94 AN: 286

European-Non Finnish (NFE) AF: 0.279 AC: 18924 AN: 67930

Other (OTH) AF: 0.291 AC: 611 AN: 2102

Alfa AF: 0.276 Hom.: 3160

Bravo AF: 0.275

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.011
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1078248; hg19: chr3-43794357;