chr5-177575088-T-C

Position:

• chr5-177575088-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_941274.3(FAM193B-DT):​n.423-31T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

FAM193B-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
FAM193B-DT	XR_941274.3	n.423-31T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.271

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

Splicing

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

Publications

LitVar

Other links and lift over

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