rs1333226

Variant names:

• chr6-137485318-T-C
• rs1333226

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 0.055 in 152,324 control chromosomes in the GnomAD database, including 416 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 0.055 (416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 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: 0.0549 AC: 8361 AN: 152204 Hom.: 414 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0550 AC: 8378 AN: 152324 Hom.: 416 Cov.: 32 AF XY: 0.0549 AC XY: 4093 AN XY: 74494

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0594

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0412 Hom.: 39

Bravo AF: 0.0594

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333226; hg19: chr6-137806455;