13-51250192-A-G

Position:

• chr13-51250192-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM124A	NM_001242312.2	c.101-1276A>G		intron_variant		ENST00000322475.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM124A	ENST00000322475.13	c.101-1276A>G		intron_variant		1	NM_001242312.2	P1
FAM124A	ENST00000615498.4	c.101-1276A>G		intron_variant		1
FAM124A	ENST00000280057.6	c.209-1276A>G		intron_variant		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

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.304

Alfa AF: 0.396 Hom.: 16797

Bravo AF: 0.295

Asia WGS AF: 0.135 AC: 473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492519; hg19: chr13-51824328; COSMIC: COSV54479752;