rs237688

Variant names:

• chr20-6300557-T-C
• rs237688

Your query was ambiguous. Multiple possible variants found:

• chr20-6300557-T-C
• chr20-6300557-T-G

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 152,046 control chromosomes in the GnomAD database, including 13,413 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 (13413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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: 0.414 AC: 62864 AN: 151928 Hom.: 13395 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.414 AC: 62915 AN: 152046 Hom.: 13413 Cov.: 32 AF XY: 0.411 AC XY: 30530 AN XY: 74310

African (AFR) AF: 0.461 AC: 19130 AN: 41460

American (AMR) AF: 0.372 AC: 5679 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3462

East Asian (EAS) AF: 0.125 AC: 645 AN: 5176

South Asian (SAS) AF: 0.398 AC: 1913 AN: 4808

European-Finnish (FIN) AF: 0.361 AC: 3818 AN: 10584

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29263 AN: 67966

Other (OTH) AF: 0.372 AC: 787 AN: 2114

Alfa AF: 0.406 Hom.: 8253

Bravo AF: 0.409

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.54
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs237688; hg19: chr20-6281204;