chr17-48969752-A-G

Variant names:

• chr17-48969752-A-G
• rs3848460

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 0.542 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.765 AC: 31721 AN: 41452

American (AMR) AF: 0.543 AC: 8280 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5174

South Asian (SAS) AF: 0.464 AC: 2233 AN: 4810

European-Finnish (FIN) AF: 0.459 AC: 4843 AN: 10542

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30618 AN: 67912

Other (OTH) AF: 0.519 AC: 1096 AN: 2112

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3848460; hg19: chr17-47047114;