rs1800481

Positions:

• chr2-21044338-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.82 in 152,108 control chromosomes in the GnomAD database, including 51,510 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.82 (51510 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.254

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 2-21044338-A-G is Benign according to our data. Variant chr2-21044338-A-G is described in ClinVar as [Benign]. Clinvar id is 3250495.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-21044338-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21044338A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124590 AN: 151990 Hom.: 51467 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.820 AC: 124687 AN: 152108 Hom.: 51510 Cov.: 32 AF XY: 0.821 AC XY: 61081 AN XY: 74364

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.816

Alfa AF: 0.818 Hom.: 4725

Bravo AF: 0.814

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial hypercholesterolemia Benign:1

Benign, criteria provided, single submitter

clinical testing

GENinCode PLC

Jun 23, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.39
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800481; hg19: chr2-21267210; COSMIC: COSV51946614;