rs2479408

Variant names:

• chr1-55038515-C-G
• rs2479408

Your query was ambiguous. Multiple possible variants found:

• chr1-55038515-C-G
• chr1-55038515-C-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 0.212 in 152,172 control chromosomes in the GnomAD database, including 3,743 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 0.21 (3743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.212 AC: 32194 AN: 152054 Hom.: 3734 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.212 AC: 32228 AN: 152172 Hom.: 3743 Cov.: 32 AF XY: 0.208 AC XY: 15442 AN XY: 74418

African (AFR) AF: 0.278 AC: 11525 AN: 41486

American (AMR) AF: 0.172 AC: 2624 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.154 AC: 745 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10594

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14253 AN: 67998

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.130 Hom.: 258

Bravo AF: 0.213

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.47
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2479408; hg19: chr1-55504188;