rs6719226

chr2-25173143-C-G

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 0.123 in 152,246 control chromosomes in the GnomAD database, including 2,175 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 0.12 (2175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.123 AC: 18762 AN: 152128 Hom.: 2174 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.123 AC: 18781 AN: 152246 Hom.: 2175 Cov.: 32 AF XY: 0.124 AC XY: 9223 AN XY: 74456

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0931 Hom.: 165

Bravo AF: 0.132

Asia WGS AF: 0.139 AC: 481 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	0.60
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6719226; hg19: chr2-25396012;