rs1440066

Variant names:

• chr2-223043492-A-C
• rs1440066

Your query was ambiguous. Multiple possible variants found:

• chr2-223043492-A-C
• chr2-223043492-A-G
• chr2-223043492-A-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 0.628 in 152,060 control chromosomes in the GnomAD database, including 30,945 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 0.63 (30945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95489 AN: 151942 Hom.: 30927 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.628 AC: 95541 AN: 152060 Hom.: 30945 Cov.: 32 AF XY: 0.636 AC XY: 47297 AN XY: 74336

African (AFR) AF: 0.472 AC: 19572 AN: 41428

American (AMR) AF: 0.710 AC: 10866 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4035 AN: 5168

South Asian (SAS) AF: 0.819 AC: 3945 AN: 4816

European-Finnish (FIN) AF: 0.723 AC: 7649 AN: 10584

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45508 AN: 67982

Other (OTH) AF: 0.618 AC: 1308 AN: 2116

Alfa AF: 0.592 Hom.: 9374

Bravo AF: 0.617

Asia WGS AF: 0.767 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs1440066; hg19: chr2-223908210;