3-5726575-T-A

Position:

• chr3-5726575-T-A

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 0.0944 in 152,254 control chromosomes in the GnomAD database, including 1,286 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 0.094 (1286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14322 AN: 152136 Hom.: 1278 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.0944 AC: 14372 AN: 152254 Hom.: 1286 Cov.: 32 AF XY: 0.0928 AC XY: 6911 AN XY: 74456

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0459

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0893

Alfa AF: 0.0720 Hom.: 97

Bravo AF: 0.102

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6782143; hg19: chr3-5768262;