rs6038571

Variant names:

• chr20-6653919-A-C
• rs6038571

Your query was ambiguous. Multiple possible variants found:

• chr20-6653919-A-C
• chr20-6653919-A-T

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 0.471 in 152,030 control chromosomes in the GnomAD database, including 18,227 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 0.47 (18227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.471 AC: 71515 AN: 151912 Hom.: 18207 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.471 AC: 71565 AN: 152030 Hom.: 18227 Cov.: 32 AF XY: 0.480 AC XY: 35642 AN XY: 74316

African (AFR) AF: 0.279 AC: 11553 AN: 41454

American (AMR) AF: 0.569 AC: 8681 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4303 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4820

European-Finnish (FIN) AF: 0.628 AC: 6645 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35218 AN: 67948

Other (OTH) AF: 0.467 AC: 988 AN: 2114

Alfa AF: 0.412 Hom.: 5442

Bravo AF: 0.460

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6038571; hg19: chr20-6634566;