20-6826629-A-C

Variant names:

• chr20-6826629-A-C
• rs2224191

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 0.117 in 152,144 control chromosomes in the GnomAD database, including 1,330 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 0.12 (1330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.117 AC: 17809 AN: 152026 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.117 AC: 17831 AN: 152144 Hom.: 1330 Cov.: 32 AF XY: 0.116 AC XY: 8608 AN XY: 74384

African (AFR) AF: 0.195 AC: 8075 AN: 41468

American (AMR) AF: 0.142 AC: 2172 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4824

European-Finnish (FIN) AF: 0.0899 AC: 953 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6073 AN: 68006

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0821 Hom.: 554

Bravo AF: 0.126

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.73
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2224191; hg19: chr20-6807276;