rs2021899

Variant names:

• chr6-170596889-G-C
• rs2021899
• ENST00000833512.1:n.107-2127C>G

Variant summary

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

The ENST00000833512.1(ENSG00000308355):​n.107-2127C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,008 control chromosomes in the GnomAD database, including 26,555 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 0.58 (26555 hom., cov: 31)
• Consequence: ENSG00000308355 ENST00000833512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 5 publications found

Genes affected

ENSG00000308355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833512.1. 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
	ENSG00000308355	ENST00000833512.1		n.107-2127C>G		intron	N/A
	ENSG00000308355	ENST00000833513.1		n.107-2127C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87945 AN: 151890 Hom.: 26503 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.579 AC: 88048 AN: 152008 Hom.: 26555 Cov.: 31 AF XY: 0.576 AC XY: 42771 AN XY: 74308

African (AFR) AF: 0.753 AC: 31200 AN: 41452

American (AMR) AF: 0.482 AC: 7366 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1753 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4083 AN: 5170

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4812

European-Finnish (FIN) AF: 0.486 AC: 5145 AN: 10576

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34267 AN: 67942

Other (OTH) AF: 0.564 AC: 1191 AN: 2112

Alfa AF: 0.548 Hom.: 2932

Bravo AF: 0.593

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.33
PhyloP100		-1.9

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: rs2021899;

hg19: chr6-170905977;