rs11732673

Variant names:

• chr4-2681328-A-G
• rs11732673
• NM_001366318.2:c.2332-8178A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-2681328-A-G
• chr4-2681328-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM193A	NM_001366318.2	c.2332-8178A>G		intron_variant	Intron 13 of 20	ENST00000637812.2	NP_001353247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM193A	ENST00000637812.2	c.2332-8178A>G		intron_variant	Intron 13 of 20	5	NM_001366318.2	ENSP00000490564.1

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

African (AFR) AF: 0.204 AC: 8158 AN: 39944

American (AMR) AF: 0.0352 AC: 516 AN: 14672

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 94 AN: 3400

East Asian (EAS) AF: 0.00180 AC: 9 AN: 4988

South Asian (SAS) AF: 0.0181 AC: 85 AN: 4684

European-Finnish (FIN) AF: 0.0216 AC: 210 AN: 9704

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0343 AC: 2275 AN: 66280

Other (OTH) AF: 0.0587 AC: 119 AN: 2028

Alfa AF: 0.0538 Hom.: 59

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
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11732673; hg19: chr4-2683055;