rs199983

Variant names:

• chr6-104412396-A-G
• rs199983
• ENST00000790145.1:n.408+463A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000790145.1(ENSG00000302865):​n.408+463A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302865 ENST00000790145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

Genes affected

ENSG00000302865 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790145.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302865	ENST00000790145.1		n.408+463A>G		intron	N/A

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

African (AFR) AF: 0.330 AC: 13258 AN: 40176

American (AMR) AF: 0.597 AC: 8920 AN: 14940

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1880 AN: 3440

East Asian (EAS) AF: 0.361 AC: 1826 AN: 5060

South Asian (SAS) AF: 0.529 AC: 2469 AN: 4670

European-Finnish (FIN) AF: 0.472 AC: 4683 AN: 9912

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42111 AN: 67380

Other (OTH) AF: 0.589 AC: 1209 AN: 2054

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs199983;

hg19: chr6-104860271;