2-100360223-A-G

Variant names:

• chr2-100360223-A-G
• rs11685401

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 0.566 in 152,074 control chromosomes in the GnomAD database, including 24,924 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 0.57 (24924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 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: 0.566 AC: 86024 AN: 151956 Hom.: 24887 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.566 AC: 86122 AN: 152074 Hom.: 24924 Cov.: 32 AF XY: 0.567 AC XY: 42169 AN XY: 74330

African (AFR) AF: 0.671 AC: 27823 AN: 41462

American (AMR) AF: 0.576 AC: 8797 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3796 AN: 5170

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4822

European-Finnish (FIN) AF: 0.526 AC: 5566 AN: 10572

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34562 AN: 67996

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.529 Hom.: 56740

Bravo AF: 0.577

Asia WGS AF: 0.635 AC: 2203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11685401; hg19: chr2-100976685;