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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM193B-DT	XR_941274.3	n.423-31T>C		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;