rs991000

Variant names:

• chr2-150457439-G-A
• rs991000

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 0.196 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.101 AC: 4215 AN: 41532

American (AMR) AF: 0.166 AC: 2530 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3466

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5184

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4826

European-Finnish (FIN) AF: 0.285 AC: 3007 AN: 10534

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17411 AN: 67972

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.217 Hom.: 3837

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

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