rs231707

Positions:

• chr4-2692658-A-G
• chr4-2692658-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.2804-928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,156 control chromosomes in the GnomAD database, including 50,984 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 0.82 (50984 hom., cov: 32)
• Consequence: FAM193A NM_001366318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM193A	NM_001366318.2	c.2804-928A>G		intron_variant		ENST00000637812.2	NP_001353247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM193A	ENST00000637812.2	c.2804-928A>G		intron_variant		5	NM_001366318.2	ENSP00000490564	A2

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124231 AN: 152038 Hom.: 50927 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.817 AC: 124349 AN: 152156 Hom.: 50984 Cov.: 32 AF XY: 0.820 AC XY: 61013 AN XY: 74368

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.833

Alfa AF: 0.830 Hom.: 53118

Bravo AF: 0.817

Asia WGS AF: 0.802 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.74

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: rs231707; hg19: chr4-2694385;