rs6890853

Variant names:

• chr5-35852209-G-A
• rs6890853

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 0.25 in 152,180 control chromosomes in the GnomAD database, including 4,948 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 0.25 (4948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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 (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.250 AC: 37994 AN: 152062 Hom.: 4948 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.250 AC: 38020 AN: 152180 Hom.: 4948 Cov.: 33 AF XY: 0.252 AC XY: 18737 AN XY: 74392

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.219

Alfa AF: 0.255 Hom.: 767

Bravo AF: 0.236

Asia WGS AF: 0.268 AC: 933 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	0.66
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6890853; hg19: chr5-35852311;