chr13-20210290-T-C

Variant names:

• chr13-20210290-T-C
• rs6490527

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 0.906 in 152,242 control chromosomes in the GnomAD database, including 62,850 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 0.91 (62850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.906 AC: 137856 AN: 152124 Hom.: 62803 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.906 AC: 137958 AN: 152242 Hom.: 62850 Cov.: 32 AF XY: 0.909 AC XY: 67699 AN XY: 74444

African (AFR) AF: 0.807 AC: 33501 AN: 41526

American (AMR) AF: 0.927 AC: 14176 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3341 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5150 AN: 5178

South Asian (SAS) AF: 0.974 AC: 4698 AN: 4824

European-Finnish (FIN) AF: 0.962 AC: 10213 AN: 10612

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63800 AN: 68024

Other (OTH) AF: 0.909 AC: 1920 AN: 2112

Alfa AF: 0.933 Hom.: 33290

Bravo AF: 0.899

Asia WGS AF: 0.974 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6490527; hg19: chr13-20784429;