rs2550956

Variant names:

• chr5-1447726-G-A
• rs2550956

Your query was ambiguous. Multiple possible variants found:

• chr5-1447726-G-A
• chr5-1447726-G-C
• chr5-1447726-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 0.208 in 152,088 control chromosomes in the GnomAD database, including 3,769 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 (3769 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.208 AC: 31614 AN: 151972 Hom.: 3757 Cov.: 33

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.208 AC: 31646 AN: 152088 Hom.: 3769 Cov.: 33 AF XY: 0.210 AC XY: 15618 AN XY: 74336

African (AFR) AF: 0.0889 AC: 3692 AN: 41546

American (AMR) AF: 0.226 AC: 3443 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.146 AC: 755 AN: 5176

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4828

European-Finnish (FIN) AF: 0.291 AC: 3066 AN: 10546

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18025 AN: 67940

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.231 Hom.: 2240

Bravo AF: 0.194

Asia WGS AF: 0.217 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.084
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2550956; hg19: chr5-1447841;