rs2206416

Variant names:

• chr20-41932203-T-C
• rs2206416
• XR_001754609.2:n.247+28108T>C

Variant summary

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

The XR_001754609.2(LOC101927182):​n.247+28108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,050 control chromosomes in the GnomAD database, including 10,848 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 0.37 (10848 hom., cov: 33)
• Consequence: LOC101927182 XR_001754609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 4 publications found

Genes affected

LOC101927182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56122 AN: 151932 Hom.: 10839 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.369 AC: 56157 AN: 152050 Hom.: 10848 Cov.: 33 AF XY: 0.375 AC XY: 27880 AN XY: 74290

African (AFR) AF: 0.257 AC: 10657 AN: 41468

American (AMR) AF: 0.418 AC: 6386 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2418 AN: 5168

South Asian (SAS) AF: 0.505 AC: 2435 AN: 4818

European-Finnish (FIN) AF: 0.428 AC: 4517 AN: 10558

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27024 AN: 67970

Other (OTH) AF: 0.377 AC: 798 AN: 2116

Alfa AF: 0.370 Hom.: 1400

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.60
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2206416; hg19: chr20-40560843;