rs461259

Variant names:

• chr5-177575088-T-C
• rs461259
• XR_941274.3:n.423-31T>C

Variant summary

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

The XR_941274.3(FAM193B-DT):​n.423-31T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,106 control chromosomes in the GnomAD database, including 6,127 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 0.27 (6127 hom., cov: 32)
• Consequence: FAM193B-DT XR_941274.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 3 publications found

Genes affected

FAM193B-DT (HGNC:55212): (FAM193B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41046 AN: 151988 Hom.: 6128 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.270 AC: 41051 AN: 152106 Hom.: 6127 Cov.: 32 AF XY: 0.270 AC XY: 20073 AN XY: 74332

African (AFR) AF: 0.146 AC: 6050 AN: 41518

American (AMR) AF: 0.239 AC: 3653 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 903 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5168

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3497 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23089 AN: 67986

Other (OTH) AF: 0.271 AC: 572 AN: 2112

Alfa AF: 0.304 Hom.: 930

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs461259; hg19: chr5-177002089; COSMIC: COSV60238206;