3-144815866-G-T

Variant names:

• chr3-144815866-G-T
• rs6799741

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 0.0446 in 151,894 control chromosomes in the GnomAD database, including 314 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 0.045 (314 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 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: 0.0445 AC: 6761 AN: 151776 Hom.: 314 Cov.: 33

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0446 AC: 6772 AN: 151894 Hom.: 314 Cov.: 33 AF XY: 0.0481 AC XY: 3569 AN XY: 74218

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.0441

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.0375

Alfa AF: 0.0189 Hom.: 45

Bravo AF: 0.0422

Asia WGS AF: 0.0810 AC: 282 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6799741; hg19: chr3-144534708;