rs6038971

chr20-7880394-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0775 in 152,252 control chromosomes in the GnomAD database, including 1,022 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 0.077 (1022 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0774 AC: 11779 AN: 152134 Hom.: 1022 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0775 AC: 11795 AN: 152252 Hom.: 1022 Cov.: 33 AF XY: 0.0804 AC XY: 5983 AN XY: 74450

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0188

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0452 Hom.: 48

Bravo AF: 0.0881

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	2.4
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038971; hg19: chr20-7861041;