rs6720869

Variant names:

• chr2-76479279-C-T
• rs6720869

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 0.229 in 152,092 control chromosomes in the GnomAD database, including 4,201 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 0.23 (4201 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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: 0.229 AC: 34785 AN: 151974 Hom.: 4198 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34799 AN: 152092 Hom.: 4201 Cov.: 33 AF XY: 0.231 AC XY: 17166 AN XY: 74338

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.225

Alfa AF: 0.227 Hom.: 572

Bravo AF: 0.219

Asia WGS AF: 0.255 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6720869; hg19: chr2-76706405;