rs211004

Positions:

• chr5-162217792-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 0.293 in 151,962 control chromosomes in the GnomAD database, including 6,963 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 0.29 (6963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44519 AN: 151840 Hom.: 6956 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.293 AC: 44561 AN: 151962 Hom.: 6963 Cov.: 32 AF XY: 0.295 AC XY: 21909 AN XY: 74268

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.263

Alfa AF: 0.287 Hom.: 782

Bravo AF: 0.293

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211004; hg19: chr5-161644798;