rs991000

chr2-150457439-G-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 0.196 in 152,106 control chromosomes in the GnomAD database, including 3,292 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 0.20 (3292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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: 0.196 AC: 29781 AN: 151988 Hom.: 3290 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.196 AC: 29802 AN: 152106 Hom.: 3292 Cov.: 32 AF XY: 0.197 AC XY: 14639 AN XY: 74358

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.182

Alfa AF: 0.235 Hom.: 2940

Bravo AF: 0.182

Asia WGS AF: 0.121 AC: 420 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.57
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991000; hg19: chr2-151313953; COSMIC: COSV50729614;