chr13-51250192-A-G

Variant names:

• chr13-51250192-A-G
• rs10492519
• NM_001242312.2:c.101-1276A>G

Variant summary

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

The NM_001242312.2(FAM124A):​c.101-1276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,962 control chromosomes in the GnomAD database, including 8,831 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 0.30 (8831 hom., cov: 33)
• Consequence: FAM124A NM_001242312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 4 publications found

Genes affected

FAM124A (HGNC:26413): (family with sequence similarity 124 member A)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242312.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM124A	NM_001242312.2	MANE Select	c.101-1276A>G		intron	N/A	NP_001229241.1	Q86V42-1
	FAM124A	NM_145019.4		c.209-1276A>G		intron	N/A	NP_659456.3
	FAM124A	NM_001330522.2		c.101-1276A>G		intron	N/A	NP_001317451.1	Q86V42-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM124A	ENST00000322475.13	TSL:1 MANE Select	c.101-1276A>G		intron	N/A	ENSP00000324625.8	Q86V42-1
	FAM124A	ENST00000615498.4	TSL:1	c.101-1276A>G		intron	N/A	ENSP00000481212.1	Q86V42-3
	FAM124A	ENST00000280057.6	TSL:2	c.209-1276A>G		intron	N/A	ENSP00000280057.6	Q86V42-2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45990 AN: 151844 Hom.: 8829 Cov.: 33

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.303 AC: 45984 AN: 151962 Hom.: 8831 Cov.: 33 AF XY: 0.301 AC XY: 22359 AN XY: 74278

African (AFR) AF: 0.0787 AC: 3268 AN: 41530

American (AMR) AF: 0.395 AC: 6028 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1113 AN: 3458

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5180

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4145 AN: 10536

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29005 AN: 67848

Other (OTH) AF: 0.304 AC: 641 AN: 2106

Alfa AF: 0.387 Hom.: 20697

Bravo AF: 0.295

Asia WGS AF: 0.135 AC: 473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492519;

hg19: chr13-51824328;

COSMIC: COSV54479752;