rs2853377

Variant names:

• chr2-232402285-G-A
• rs2853377

Your query was ambiguous. Multiple possible variants found:

• chr2-232402285-G-A
• chr2-232402285-G-C

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 0.361 in 147,900 control chromosomes in the GnomAD database, including 9,650 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 0.36 (9650 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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: 0.361 AC: 53293 AN: 147784 Hom.: 9631 Cov.: 26

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.412

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.361 AC: 53339 AN: 147900 Hom.: 9650 Cov.: 26 AF XY: 0.357 AC XY: 25645 AN XY: 71912

African (AFR) AF: 0.363 AC: 14679 AN: 40398

American (AMR) AF: 0.296 AC: 4341 AN: 14690

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1413 AN: 3430

East Asian (EAS) AF: 0.331 AC: 1556 AN: 4708

South Asian (SAS) AF: 0.279 AC: 1210 AN: 4342

European-Finnish (FIN) AF: 0.332 AC: 3249 AN: 9780

Middle Eastern (MID) AF: 0.426 AC: 121 AN: 284

European-Non Finnish (NFE) AF: 0.379 AC: 25532 AN: 67306

Other (OTH) AF: 0.380 AC: 779 AN: 2052

Alfa AF: 0.348 Hom.: 1132

Bravo AF: 0.353

Asia WGS AF: 0.269 AC: 938 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2853377; hg19: chr2-233266995;