rs11732673

chr4-2681328-A-Gchr4-2681328-A-T

Variant summary

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

The NM_001366318.2(FAM193A):c.2332-8178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 146,884 control chromosomes in the GnomAD database, including 883 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 0.078 (883 hom., cov: 32)
• Consequence: FAM193A NM_001366318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

FAM193A (HGNC:16822): (family with sequence similarity 193 member A)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM193A	NM_001366318.2	c.2332-8178A>G		intron_variant		ENST00000637812.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM193A	ENST00000637812.2	c.2332-8178A>G		intron_variant		5	NM_001366318.2	A2

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11458 AN: 146784 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.00448

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.00180

Gnomad SAS AF: 0.0183

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0782 AC: 11483 AN: 146884 Hom.: 883 Cov.: 32 AF XY: 0.0765 AC XY: 5472 AN XY: 71502

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.00180

Gnomad4 SAS AF: 0.0181

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0343

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0483 Hom.: 47

Bravo AF: 0.0823

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.1
Dann	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11732673; hg19: chr4-2683055;