rs2239341

chr16-24254852-A-C

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 0.265 in 152,126 control chromosomes in the GnomAD database, including 5,479 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 0.26 (5479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 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: 0.265 AC: 40240 AN: 152008 Hom.: 5478 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.265 AC: 40253 AN: 152126 Hom.: 5479 Cov.: 32 AF XY: 0.267 AC XY: 19898 AN XY: 74388

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.289

Alfa AF: 0.259 Hom.: 703

Bravo AF: 0.269

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	9.0
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: rs2239341; hg19: chr16-24266173;