chr3-136206349-T-A

Variant names:

• chr3-136206349-T-A
• rs1154988

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 0.762 in 152,182 control chromosomes in the GnomAD database, including 44,414 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 0.76 (44414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.762 AC: 115853 AN: 152064 Hom.: 44378 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.762 AC: 115948 AN: 152182 Hom.: 44414 Cov.: 33 AF XY: 0.765 AC XY: 56950 AN XY: 74416

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.746

Alfa AF: 0.772 Hom.: 5664

Bravo AF: 0.752

Asia WGS AF: 0.818 AC: 2842 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154988; hg19: chr3-135925191;