rs2179357

Variant names:

• chr20-46742445-T-C
• rs2179357
• XR_007067616.1:n.*170T>C

Variant summary

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

The XR_007067616.1(LOC124904918):​n.*170T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,914 control chromosomes in the GnomAD database, including 12,416 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 0.40 (12416 hom., cov: 31)
• Consequence: LOC124904918 XR_007067616.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 6 publications found

Genes affected

LOC124904918 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.397 AC: 60233 AN: 151794 Hom.: 12385 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.397 AC: 60318 AN: 151914 Hom.: 12416 Cov.: 31 AF XY: 0.405 AC XY: 30054 AN XY: 74278

African (AFR) AF: 0.340 AC: 14075 AN: 41422

American (AMR) AF: 0.523 AC: 7986 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3251 AN: 5148

South Asian (SAS) AF: 0.407 AC: 1957 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4564 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26107 AN: 67924

Other (OTH) AF: 0.406 AC: 855 AN: 2106

Alfa AF: 0.392 Hom.: 16651

Bravo AF: 0.402

Asia WGS AF: 0.499 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.36
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2179357; hg19: chr20-45371084;