rs847126

chr2-176072106-A-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 0.393 in 152,094 control chromosomes in the GnomAD database, including 15,126 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 0.39 (15126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.393 AC: 59696 AN: 151976 Hom.: 15092 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.393 AC: 59792 AN: 152094 Hom.: 15126 Cov.: 32 AF XY: 0.392 AC XY: 29117 AN XY: 74356

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.372

Alfa AF: 0.283 Hom.: 10782

Bravo AF: 0.413

Asia WGS AF: 0.363 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.22
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847126; hg19: chr2-176936834;