chr2-35222568-A-G

Variant names:

• chr2-35222568-A-G
• rs6707443

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 0.159 in 151,836 control chromosomes in the GnomAD database, including 2,290 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 0.16 (2290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.159 AC: 24189 AN: 151718 Hom.: 2293 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0280

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.159 AC: 24179 AN: 151836 Hom.: 2290 Cov.: 32 AF XY: 0.155 AC XY: 11538 AN XY: 74230

African (AFR) AF: 0.0747 AC: 3099 AN: 41492

American (AMR) AF: 0.141 AC: 2152 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3464

East Asian (EAS) AF: 0.0282 AC: 145 AN: 5140

South Asian (SAS) AF: 0.142 AC: 685 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1793 AN: 10596

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14842 AN: 67790

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.182 Hom.: 346

Bravo AF: 0.153

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.70
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6707443; hg19: chr2-35447634;