rs4661280

Variant names:

• chr1-223108367-C-A
• rs4661280

Your query was ambiguous. Multiple possible variants found:

• chr1-223108367-C-A
• chr1-223108367-C-G

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 0.337 in 151,918 control chromosomes in the GnomAD database, including 9,940 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 (9940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.337 AC: 51208 AN: 151800 Hom.: 9939 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.337 AC: 51236 AN: 151918 Hom.: 9940 Cov.: 32 AF XY: 0.340 AC XY: 25239 AN XY: 74246

African (AFR) AF: 0.145 AC: 6021 AN: 41522

American (AMR) AF: 0.324 AC: 4942 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5178

South Asian (SAS) AF: 0.422 AC: 2026 AN: 4798

European-Finnish (FIN) AF: 0.497 AC: 5226 AN: 10518

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29273 AN: 67850

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.224 Hom.: 1131

Bravo AF: 0.313

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.93
DANN	Benign	0.33
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4661280; hg19: chr1-223281709;