rs3848460

Variant names:

• chr17-48969752-A-G
• rs3848460

Your query was ambiguous. Multiple possible variants found:

• chr17-48969752-A-G
• chr17-48969752-A-T

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 0.542 in 151,918 control chromosomes in the GnomAD database, including 23,977 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 0.54 (23977 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.542 AC: 82228 AN: 151800 Hom.: 23922 Cov.: 30

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.542 AC: 82350 AN: 151918 Hom.: 23977 Cov.: 30 AF XY: 0.541 AC XY: 40148 AN XY: 74264

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.519

Alfa AF: 0.505 Hom.: 3313

Bravo AF: 0.556

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3848460; hg19: chr17-47047114;