20-7837614-G-T

Variant names:

• chr20-7837614-G-T
• rs2423290

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 151,938 control chromosomes in the GnomAD database, including 6,517 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 (6517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43438 AN: 151820 Hom.: 6494 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.286 AC: 43507 AN: 151938 Hom.: 6517 Cov.: 32 AF XY: 0.286 AC XY: 21254 AN XY: 74284

African (AFR) AF: 0.329 AC: 13657 AN: 41470

American (AMR) AF: 0.304 AC: 4638 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3466

East Asian (EAS) AF: 0.326 AC: 1676 AN: 5144

South Asian (SAS) AF: 0.486 AC: 2336 AN: 4804

European-Finnish (FIN) AF: 0.205 AC: 2167 AN: 10550

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16857 AN: 67918

Other (OTH) AF: 0.313 AC: 661 AN: 2110

Alfa AF: 0.269 Hom.: 4862

Bravo AF: 0.294

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.66
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2423290; hg19: chr20-7818261;