rs6884962

chr5-173255379-G-Achr5-173255379-G-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 0.41 in 151,248 control chromosomes in the GnomAD database, including 13,227 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 0.41 (13227 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.410 AC: 62020 AN: 151136 Hom.: 13212 Cov.: 33

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.410 AC: 62075 AN: 151248 Hom.: 13227 Cov.: 33 AF XY: 0.417 AC XY: 30859 AN XY: 73916

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.414

Alfa AF: 0.359 Hom.: 11380

Bravo AF: 0.421

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6884962; hg19: chr5-172682382;