rs2248160

Variant names:

• chr14-28004983-A-G
• rs2248160

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 0.0464 in 152,022 control chromosomes in the GnomAD database, including 255 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 0.046 (255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7048 AN: 151904 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0342

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00894

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0464 AC: 7050 AN: 152022 Hom.: 255 Cov.: 32 AF XY: 0.0449 AC XY: 3339 AN XY: 74284

African (AFR) AF: 0.0131 AC: 545 AN: 41488

American (AMR) AF: 0.0341 AC: 521 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.00874 AC: 42 AN: 4806

European-Finnish (FIN) AF: 0.0761 AC: 803 AN: 10552

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0685 AC: 4659 AN: 67974

Other (OTH) AF: 0.0602 AC: 127 AN: 2108

Alfa AF: 0.0595 Hom.: 400

Bravo AF: 0.0437

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.57
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2248160; hg19: chr14-28474189;