rs844438

chr3-57987953-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 0.381 in 152,012 control chromosomes in the GnomAD database, including 11,407 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 (11407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.538 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: 0.381 AC: 57919 AN: 151894 Hom.: 11391 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.381 AC: 57964 AN: 152012 Hom.: 11407 Cov.: 32 AF XY: 0.387 AC XY: 28786 AN XY: 74292

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.394

Alfa AF: 0.381 Hom.: 1393

Bravo AF: 0.377

Asia WGS AF: 0.483 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.30
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844438; hg19: chr3-57973680;