20-7587211-C-G

Variant names:

• chr20-7587211-C-G
• rs6108015

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 0.414 in 151,720 control chromosomes in the GnomAD database, including 13,335 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 0.41 (13335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.414 AC: 62710 AN: 151602 Hom.: 13322 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.414 AC: 62754 AN: 151720 Hom.: 13335 Cov.: 32 AF XY: 0.415 AC XY: 30721 AN XY: 74102

African (AFR) AF: 0.472 AC: 19549 AN: 41394

American (AMR) AF: 0.333 AC: 5067 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2761 AN: 5124

South Asian (SAS) AF: 0.491 AC: 2360 AN: 4808

European-Finnish (FIN) AF: 0.435 AC: 4566 AN: 10500

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26219 AN: 67888

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.239 Hom.: 513

Bravo AF: 0.404

Asia WGS AF: 0.484 AC: 1682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.33
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs6108015; hg19: chr20-7567858;