rs2248160

Variant names:

• chr14-28004983-A-G
• rs2248160

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0464 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

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0341

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00874

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.0602

Alfa AF: 0.0622 Hom.: 320

Bravo AF: 0.0437

Asia WGS AF: 0.0140 AC: 49 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	4.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2248160; hg19: chr14-28474189;