rs268706

Variant names:

• chr5-33405491-G-A
• rs268706

Your query was ambiguous. Multiple possible variants found:

• chr5-33405491-G-A
• chr5-33405491-G-C

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 0.167 in 152,048 control chromosomes in the GnomAD database, including 2,302 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 0.17 (2302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 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: 0.167 AC: 25310 AN: 151932 Hom.: 2299 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.167 AC: 25318 AN: 152048 Hom.: 2302 Cov.: 31 AF XY: 0.171 AC XY: 12742 AN XY: 74306

African (AFR) AF: 0.129 AC: 5345 AN: 41494

American (AMR) AF: 0.255 AC: 3900 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1385 AN: 5142

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4814

European-Finnish (FIN) AF: 0.204 AC: 2152 AN: 10562

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.152 AC: 10342 AN: 67980

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.162 Hom.: 9407

Bravo AF: 0.172

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.64
DANN	Benign	0.26
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs268706; hg19: chr5-33405597;