3-135341215-C-T

Position:

• chr3-135341215-C-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 0.74 in 151,966 control chromosomes in the GnomAD database, including 42,120 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 0.74 (42120 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135341215C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000240086	ENST00000649588.1	n.108-80156G>A		intron_variant
ENSG00000240086	ENST00000655873.1	n.366+38047G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112420 AN: 151848 Hom.: 42070 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.740 AC: 112522 AN: 151966 Hom.: 42120 Cov.: 31 AF XY: 0.734 AC XY: 54537 AN XY: 74276

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.743

Alfa AF: 0.702 Hom.: 17250

Bravo AF: 0.759

Asia WGS AF: 0.674 AC: 2343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs823968; hg19: chr3-135060057;