rs1333226

Positions:

• chr6-137485318-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;