rs2199870

Positions:

• chr6-32805395-C-T

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 0.672 in 151,792 control chromosomes in the GnomAD database, including 34,469 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 0.67 (34469 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32805395C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101905 AN: 151676 Hom.: 34462 Cov.: 30

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.672 AC: 101948 AN: 151792 Hom.: 34469 Cov.: 30 AF XY: 0.679 AC XY: 50333 AN XY: 74168

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.682

Alfa AF: 0.661 Hom.: 18353

Bravo AF: 0.657

Asia WGS AF: 0.749 AC: 2605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2199870; hg19: chr6-32773172;