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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904918	XR_007067616.1	n.*170T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;