rs1337918

Variant names:

• chr20-22586970-C-A
• rs1337918

Your query was ambiguous. Multiple possible variants found:

• chr20-22586970-C-A
• chr20-22586970-C-G

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 0.135 in 152,016 control chromosomes in the GnomAD database, including 2,932 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 0.14 (2932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.135 AC: 20522 AN: 151898 Hom.: 2914 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.135 AC: 20575 AN: 152016 Hom.: 2932 Cov.: 32 AF XY: 0.132 AC XY: 9821 AN XY: 74318

African (AFR) AF: 0.355 AC: 14686 AN: 41358

American (AMR) AF: 0.0664 AC: 1015 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.158 AC: 809 AN: 5122

South Asian (SAS) AF: 0.0921 AC: 444 AN: 4820

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10622

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0396 AC: 2693 AN: 68020

Other (OTH) AF: 0.121 AC: 254 AN: 2106

Alfa AF: 0.0339 Hom.: 64

Bravo AF: 0.149

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.7
DANN	Benign	0.44
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1337918; hg19: chr20-22567608;