rs382925

Positions:

• chr2-70579237-C-T

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 0.338 in 151,944 control chromosomes in the GnomAD database, including 9,202 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 0.34 (9202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51259 AN: 151826 Hom.: 9184 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.338 AC: 51308 AN: 151944 Hom.: 9202 Cov.: 31 AF XY: 0.344 AC XY: 25586 AN XY: 74272

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.322

Alfa AF: 0.348 Hom.: 1778

Bravo AF: 0.325

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
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: rs382925; hg19: chr2-70806369;