20-7838785-T-C

Variant names:

• chr20-7838785-T-C
• rs2423292

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 0.286 in 152,000 control chromosomes in the GnomAD database, including 6,507 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 0.29 (6507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 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: 0.286 AC: 43405 AN: 151882 Hom.: 6484 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.286 AC: 43474 AN: 152000 Hom.: 6507 Cov.: 32 AF XY: 0.286 AC XY: 21243 AN XY: 74314

African (AFR) AF: 0.329 AC: 13631 AN: 41462

American (AMR) AF: 0.303 AC: 4635 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5158

South Asian (SAS) AF: 0.486 AC: 2341 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2167 AN: 10564

Middle Eastern (MID) AF: 0.292 AC: 84 AN: 288

European-Non Finnish (NFE) AF: 0.248 AC: 16858 AN: 67940

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.261 Hom.: 2318

Bravo AF: 0.294

Asia WGS AF: 0.442 AC: 1525 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2423292; hg19: chr20-7819432;