20-7326318-C-G

Variant names:

• chr20-7326318-C-G
• rs2224053

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 0.321 in 151,970 control chromosomes in the GnomAD database, including 8,866 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 0.32 (8866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.424 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: 0.321 AC: 48818 AN: 151852 Hom.: 8863 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.321 AC: 48829 AN: 151970 Hom.: 8866 Cov.: 32 AF XY: 0.322 AC XY: 23945 AN XY: 74258

African (AFR) AF: 0.145 AC: 6016 AN: 41478

American (AMR) AF: 0.433 AC: 6596 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.384 AC: 1969 AN: 5128

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4824

European-Finnish (FIN) AF: 0.327 AC: 3452 AN: 10554

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26665 AN: 67964

Other (OTH) AF: 0.358 AC: 755 AN: 2110

Alfa AF: 0.228 Hom.: 548

Bravo AF: 0.321

Asia WGS AF: 0.364 AC: 1260 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	0.20
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2224053; hg19: chr20-7306965;