rs199983

Variant names:

• chr6-104412396-A-G
• rs199983

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 0.518 in 148,828 control chromosomes in the GnomAD database, including 21,325 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 0.52 (21325 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.518 AC: 77106 AN: 148736 Hom.: 21325 Cov.: 24

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.518 AC: 77112 AN: 148828 Hom.: 21325 Cov.: 24 AF XY: 0.511 AC XY: 37092 AN XY: 72534

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.589

Alfa AF: 0.538 Hom.: 2526

Bravo AF: 0.520

Asia WGS AF: 0.453 AC: 1573 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199983; hg19: chr6-104860271;