rs912991

Variant names:

• chr1-5298324-A-G
• rs912991

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 0.437 in 152,066 control chromosomes in the GnomAD database, including 14,877 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 0.44 (14877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437

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 = 0.658 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: 0.437 AC: 66459 AN: 151946 Hom.: 14856 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.437 AC: 66522 AN: 152066 Hom.: 14877 Cov.: 33 AF XY: 0.446 AC XY: 33114 AN XY: 74318

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.445

Alfa AF: 0.436 Hom.: 20349

Bravo AF: 0.425

Asia WGS AF: 0.574 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912991; hg19: chr1-5358384;