chr2-5523876-G-T

Variant names:

• chr2-5523876-G-T
• rs11894081

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 0.579 in 151,956 control chromosomes in the GnomAD database, including 29,398 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 0.58 (29398 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 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: 0.579 AC: 87942 AN: 151838 Hom.: 29392 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.579 AC: 87956 AN: 151956 Hom.: 29398 Cov.: 33 AF XY: 0.575 AC XY: 42692 AN XY: 74284

African (AFR) AF: 0.223 AC: 9256 AN: 41450

American (AMR) AF: 0.723 AC: 11053 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2260 AN: 3472

East Asian (EAS) AF: 0.568 AC: 2932 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2766 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6560 AN: 10544

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50940 AN: 67922

Other (OTH) AF: 0.620 AC: 1307 AN: 2108

Alfa AF: 0.670 Hom.: 59193

Bravo AF: 0.575

Asia WGS AF: 0.556 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11894081; hg19: chr2-5664008;