3-135868969-T-C

Variant names:

• chr3-135868969-T-C
• rs1401543

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.247 in 151,956 control chromosomes in the GnomAD database, including 5,322 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 0.25 (5322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.247 AC: 37496 AN: 151838 Hom.: 5309 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.247 AC: 37546 AN: 151956 Hom.: 5322 Cov.: 32 AF XY: 0.246 AC XY: 18298 AN XY: 74266

African (AFR) AF: 0.377 AC: 15622 AN: 41432

American (AMR) AF: 0.156 AC: 2383 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3472

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5164

South Asian (SAS) AF: 0.159 AC: 767 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2947 AN: 10544

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14437 AN: 67960

Other (OTH) AF: 0.226 AC: 477 AN: 2112

Alfa AF: 0.213 Hom.: 10090

Bravo AF: 0.243

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1401543; hg19: chr3-135587811;