rs1800481

Variant names:

• chr2-21044338-A-G
• rs1800481
• ENST00000762416.1:n.149A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-21044338-A-G
• chr2-21044338-A-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000762416.1(ENSG00000299295):​n.149A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299295 ENST00000762416.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.254
• Publications: 9 publications found

Genes affected

ENSG00000299295 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId is 3250495.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762416.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299295	ENST00000762416.1		n.149A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000299295	ENST00000762411.1		n.73-580A>G		intron	N/A
	ENSG00000299295	ENST00000762412.1		n.187-580A>G		intron	N/A

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

African (AFR) AF: 0.724 AC: 30041 AN: 41494

American (AMR) AF: 0.855 AC: 13079 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2413 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5101 AN: 5120

South Asian (SAS) AF: 0.873 AC: 4199 AN: 4810

European-Finnish (FIN) AF: 0.858 AC: 9095 AN: 10602

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57975 AN: 67986

Other (OTH) AF: 0.816 AC: 1723 AN: 2112

Alfa AF: 0.851 Hom.: 13162

Bravo AF: 0.814

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Familial hypercholesterolemia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.39
DANN	Benign	0.20
PhyloP100		-0.25
PromoterAI		0.022	Neutral

Splicing

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

Other links and lift over

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