chr3-144621363-C-T

Variant names:

• chr3-144621363-C-T
• rs800082

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 0.378 in 152,030 control chromosomes in the GnomAD database, including 11,559 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 0.38 (11559 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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: 0.378 AC: 57458 AN: 151912 Hom.: 11546 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.378 AC: 57501 AN: 152030 Hom.: 11559 Cov.: 33 AF XY: 0.380 AC XY: 28241 AN XY: 74302

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.382

Alfa AF: 0.421 Hom.: 30387

Bravo AF: 0.365

Asia WGS AF: 0.315 AC: 1094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs800082; hg19: chr3-144340205;