rs847153

Positions:

• chr2-176098261-G-A
• chr2-176098261-G-C

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 0.39 in 152,126 control chromosomes in the GnomAD database, including 12,939 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 (12939 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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: 0.390 AC: 59274 AN: 152008 Hom.: 12907 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.390 AC: 59358 AN: 152126 Hom.: 12939 Cov.: 33 AF XY: 0.382 AC XY: 28434 AN XY: 74370

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.367

Alfa AF: 0.338 Hom.: 13912

Bravo AF: 0.408

Asia WGS AF: 0.214 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847153; hg19: chr2-176962989;