rs6716573

Positions:

• chr2-113283164-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 0.265 in 152,182 control chromosomes in the GnomAD database, including 5,449 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 0.27 (5449 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113283164C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40285 AN: 152064 Hom.: 5435 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.265 AC: 40334 AN: 152182 Hom.: 5449 Cov.: 33 AF XY: 0.264 AC XY: 19665 AN XY: 74406

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.288

Alfa AF: 0.271 Hom.: 1307

Bravo AF: 0.266

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6716573; hg19: chr2-114040741;