rs382925

Variant names:

• chr2-70579237-C-T
• rs382925

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 0.338 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.237 AC: 9800 AN: 41398

American (AMR) AF: 0.381 AC: 5823 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1853 AN: 5172

South Asian (SAS) AF: 0.361 AC: 1734 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5090 AN: 10538

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24983 AN: 67958

Other (OTH) AF: 0.322 AC: 680 AN: 2112

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs382925; hg19: chr2-70806369;