chr3-194685159-G-T

Variant names:

• chr3-194685159-G-T
• rs789859
• XM_047449428.1:c.475+179C>A

Variant summary

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

The XM_047449428.1(LOC124909474):​c.475+179C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,024 control chromosomes in the GnomAD database, including 14,257 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 0.42 (14257 hom., cov: 32)
• Consequence: LOC124909474 XM_047449428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 16 publications found

Genes affected

LOC124909474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64560 AN: 151902 Hom.: 14238 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.425 AC: 64601 AN: 152024 Hom.: 14257 Cov.: 32 AF XY: 0.420 AC XY: 31176 AN XY: 74284

African (AFR) AF: 0.526 AC: 21796 AN: 41458

American (AMR) AF: 0.374 AC: 5725 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1110 AN: 5172

South Asian (SAS) AF: 0.338 AC: 1632 AN: 4826

European-Finnish (FIN) AF: 0.361 AC: 3798 AN: 10522

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27758 AN: 67968

Other (OTH) AF: 0.430 AC: 907 AN: 2110

Alfa AF: 0.403 Hom.: 34305

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs789859; hg19: chr3-194405888;