rs2854184

chr17-63920633-T-Achr17-63920633-T-G

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 0.329 in 152,152 control chromosomes in the GnomAD database, including 9,377 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 0.33 (9377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 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: 0.329 AC: 49989 AN: 152034 Hom.: 9372 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.329 AC: 50018 AN: 152152 Hom.: 9377 Cov.: 32 AF XY: 0.326 AC XY: 24263 AN XY: 74368

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.366

Alfa AF: 0.258 Hom.: 730

Bravo AF: 0.321

Asia WGS AF: 0.335 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.8
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2854184; hg19: chr17-61997993;