chr2-53226706-A-G

Variant names:

• chr2-53226706-A-G
• rs6758455

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 0.0952 in 152,226 control chromosomes in the GnomAD database, including 685 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 0.095 (685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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: 0.0952 AC: 14488 AN: 152108 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0952 AC: 14489 AN: 152226 Hom.: 685 Cov.: 32 AF XY: 0.0936 AC XY: 6965 AN XY: 74420

African (AFR) AF: 0.114 AC: 4730 AN: 41530

American (AMR) AF: 0.0642 AC: 982 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3470

East Asian (EAS) AF: 0.0435 AC: 225 AN: 5174

South Asian (SAS) AF: 0.0577 AC: 279 AN: 4834

European-Finnish (FIN) AF: 0.0830 AC: 880 AN: 10606

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0983 AC: 6681 AN: 67994

Other (OTH) AF: 0.104 AC: 220 AN: 2116

Alfa AF: 0.0964 Hom.: 1339

Bravo AF: 0.0940

Asia WGS AF: 0.0650 AC: 227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6758455; hg19: chr2-53453844;