rs6705593

Positions:

• chr2-203906791-C-G
• chr2-203906791-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 0.438 in 151,830 control chromosomes in the GnomAD database, including 14,855 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 0.44 (14855 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.203906791C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66466 AN: 151712 Hom.: 14850 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.438 AC: 66494 AN: 151830 Hom.: 14855 Cov.: 32 AF XY: 0.433 AC XY: 32145 AN XY: 74164

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.463

Alfa AF: 0.308 Hom.: 737

Bravo AF: 0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6705593; hg19: chr2-204771514;