rs10516823

Variant names:

• chr4-88876487-G-A
• rs10516823
• NM_014883.4:c.844-25304C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-88876487-G-A
• chr4-88876487-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014883.4(FAM13A):​c.844-25304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,034 control chromosomes in the GnomAD database, including 704 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 0.094 (704 hom., cov: 32)
• Consequence: FAM13A NM_014883.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 2 publications found

Genes affected

FAM13A (HGNC:19367): (family with sequence similarity 13 member A) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13A	NM_014883.4	c.844-25304C>T		intron_variant	Intron 6 of 23	ENST00000264344.10	NP_055698.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13A	ENST00000264344.10	c.844-25304C>T		intron_variant	Intron 6 of 23	5	NM_014883.4	ENSP00000264344.5

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14203 AN: 151916 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0935 AC: 14221 AN: 152034 Hom.: 704 Cov.: 32 AF XY: 0.0942 AC XY: 7001 AN XY: 74308

African (AFR) AF: 0.0910 AC: 3773 AN: 41472

American (AMR) AF: 0.0866 AC: 1323 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3464

East Asian (EAS) AF: 0.128 AC: 662 AN: 5154

South Asian (SAS) AF: 0.0977 AC: 469 AN: 4802

European-Finnish (FIN) AF: 0.0771 AC: 815 AN: 10570

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6494 AN: 67986

Other (OTH) AF: 0.0984 AC: 207 AN: 2104

Alfa AF: 0.0918 Hom.: 989

Bravo AF: 0.0937

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.25
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: rs10516823; hg19: chr4-89797638;