rs6719226

Variant names:

• chr2-25173143-C-G
• rs6719226

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.304 AC: 12609 AN: 41516

American (AMR) AF: 0.0603 AC: 922 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3470

East Asian (EAS) AF: 0.0946 AC: 491 AN: 5188

South Asian (SAS) AF: 0.169 AC: 814 AN: 4826

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0441 AC: 2998 AN: 68022

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

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
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6719226; hg19: chr2-25396012;