rs2243827

Variant names:

• chr17-58281580-G-T
• rs2243827

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 0.127 in 152,222 control chromosomes in the GnomAD database, including 1,410 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 0.13 (1410 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.127 AC: 19351 AN: 152104 Hom.: 1409 Cov.: 31

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.127 AC: 19351 AN: 152222 Hom.: 1410 Cov.: 31 AF XY: 0.125 AC XY: 9281 AN XY: 74412

African (AFR) AF: 0.0806 AC: 3350 AN: 41552

American (AMR) AF: 0.138 AC: 2102 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10996 AN: 68002

Other (OTH) AF: 0.156 AC: 329 AN: 2108

Alfa AF: 0.116 Hom.: 250

Bravo AF: 0.127

Asia WGS AF: 0.0250 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.53
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2243827; hg19: chr17-56358941;