rs912991

Variant names:

• chr1-5298324-A-G
• rs912991

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 0.437 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
• Publications: 2 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 = 0.658 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

African (AFR) AF: 0.377 AC: 15632 AN: 41458

American (AMR) AF: 0.441 AC: 6752 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3493 AN: 5158

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5652 AN: 10562

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29603 AN: 67980

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.436 Hom.: 28107

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs912991; hg19: chr1-5358384;