rs1408501

Variant names:

• chr6-33824153-A-G
• rs1408501

Your query was ambiguous. Multiple possible variants found:

• chr6-33824153-A-G
• chr6-33824153-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 0.118 in 152,294 control chromosomes in the GnomAD database, including 1,271 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 0.12 (1271 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17916 AN: 152176 Hom.: 1268 Cov.: 33

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.118 AC: 17933 AN: 152294 Hom.: 1271 Cov.: 33 AF XY: 0.117 AC XY: 8702 AN XY: 74468

African (AFR) AF: 0.0606 AC: 2519 AN: 41578

American (AMR) AF: 0.109 AC: 1669 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3466

East Asian (EAS) AF: 0.0212 AC: 110 AN: 5186

South Asian (SAS) AF: 0.121 AC: 584 AN: 4826

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10616

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10379 AN: 67994

Other (OTH) AF: 0.117 AC: 248 AN: 2116

Alfa AF: 0.126 Hom.: 1321

Bravo AF: 0.109

Asia WGS AF: 0.0850 AC: 300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1408501; hg19: chr6-33791930;