rs13040307

Variant names:

• chr20-46114008-C-T
• rs13040307

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 0.19 in 152,126 control chromosomes in the GnomAD database, including 3,275 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 0.19 (3275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.190 AC: 28925 AN: 152008 Hom.: 3269 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.190 AC: 28937 AN: 152126 Hom.: 3275 Cov.: 32 AF XY: 0.192 AC XY: 14292 AN XY: 74350

African (AFR) AF: 0.0665 AC: 2760 AN: 41514

American (AMR) AF: 0.162 AC: 2473 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1480 AN: 5168

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4816

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10576

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16379 AN: 67984

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.212 Hom.: 1363

Bravo AF: 0.179

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13040307; hg19: chr20-44742647;