rs844438

Variant names:

• chr3-57987953-T-A
• rs844438

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;