rs17103248

Positions:

• chr14-66049950-G-A

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 0.237 in 152,076 control chromosomes in the GnomAD database, including 4,370 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 0.24 (4370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35991 AN: 151958 Hom.: 4366 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.237 AC: 36022 AN: 152076 Hom.: 4370 Cov.: 32 AF XY: 0.239 AC XY: 17750 AN XY: 74330

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.215

Alfa AF: 0.234 Hom.: 2119

Bravo AF: 0.230

Asia WGS AF: 0.299 AC: 1038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17103248; hg19: chr14-66516668;