rs223661

Variant names:

• chr2-31791920-G-A
• rs223661

Your query was ambiguous. Multiple possible variants found:

• chr2-31791920-G-A
• chr2-31791920-G-T

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 0.442 in 151,974 control chromosomes in the GnomAD database, including 15,072 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 0.44 (15072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67160 AN: 151856 Hom.: 15067 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.442 AC: 67187 AN: 151974 Hom.: 15072 Cov.: 32 AF XY: 0.443 AC XY: 32905 AN XY: 74284

African (AFR) AF: 0.405 AC: 16764 AN: 41408

American (AMR) AF: 0.445 AC: 6802 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5160

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4812

European-Finnish (FIN) AF: 0.537 AC: 5672 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31830 AN: 67972

Other (OTH) AF: 0.430 AC: 904 AN: 2102

Alfa AF: 0.456 Hom.: 1924

Bravo AF: 0.433

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.28
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs223661; hg19: chr2-32016989;