rs6038971

Variant names:

• chr20-7880394-A-G
• rs6038971

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;