rs2853933

Positions:

• chr6-31286311-T-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 0.658 in 152,094 control chromosomes in the GnomAD database, including 33,225 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 0.66 (33225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.658 AC: 99931 AN: 151976 Hom.: 33184 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.658 AC: 100025 AN: 152094 Hom.: 33225 Cov.: 32 AF XY: 0.663 AC XY: 49243 AN XY: 74328

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.681

Alfa AF: 0.607 Hom.: 41450

Bravo AF: 0.666

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853933; hg19: chr6-31254088;