rs6884905

Variant names:

• chr5-10148309-C-T
• rs6884905

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 0.122 in 152,212 control chromosomes in the GnomAD database, including 1,242 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 0.12 (1242 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18504 AN: 152094 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.122 AC: 18523 AN: 152212 Hom.: 1242 Cov.: 32 AF XY: 0.120 AC XY: 8915 AN XY: 74412

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0926

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.115

Alfa AF: 0.130 Hom.: 267

Bravo AF: 0.120

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.064
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: rs6884905; hg19: chr5-10148421;