rs1408501

Positions:

• chr6-33824153-A-G
• chr6-33824153-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0212

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.117

Alfa AF: 0.132 Hom.: 696

Bravo AF: 0.109

Asia WGS AF: 0.0850 AC: 300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408501; hg19: chr6-33791930;