3-144815866-G-T

Variant names:

• chr3-144815866-G-T
• rs6799741

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 0.0446 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0963 AC: 3990 AN: 41434

American (AMR) AF: 0.0246 AC: 374 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 72 AN: 3468

East Asian (EAS) AF: 0.108 AC: 559 AN: 5164

South Asian (SAS) AF: 0.0992 AC: 479 AN: 4828

European-Finnish (FIN) AF: 0.0441 AC: 464 AN: 10530

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 740 AN: 67924

Other (OTH) AF: 0.0375 AC: 79 AN: 2106

Alfa AF: 0.0193 Hom.: 55

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6799741; hg19: chr3-144534708;