rs13150445

chr4-38929476-A-Cchr4-38929476-A-Gchr4-38929476-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138389.4(FAM114A1):c.1161+143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 641,218 control chromosomes in the GnomAD database, including 23,519 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 0.24 (5044 hom., cov: 33)
  • Exomes 𝑓: 0.25 (18475 hom.)
• Consequence: FAM114A1 NM_138389.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

FAM114A1 (HGNC:25087): (family with sequence similarity 114 member A1) The protein encoded by this gene belongs to the FAM114 family and may play a role in neuronal cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -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 = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM114A1	NM_138389.4	c.1161+143A>C		intron_variant		ENST00000358869.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM114A1	ENST00000358869.5	c.1161+143A>C		intron_variant		1	NM_138389.4	P1
FAM114A1	ENST00000508737.1	n.235+143A>C		intron_variant, non_coding_transcript_variant		1
FAM114A1	ENST00000515037.5	c.540+143A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37274 AN: 152092 Hom.: 5036 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.249 AC: 121597 AN: 489008 Hom.: 18475 AF XY: 0.257 AC XY: 66133 AN XY: 257760

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.298

Gnomad4 ASJ exome AF: 0.332

Gnomad4 EAS exome AF: 0.552

Gnomad4 SAS exome AF: 0.413

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.245 AC: 37283 AN: 152210 Hom.: 5044 Cov.: 33 AF XY: 0.246 AC XY: 18287 AN XY: 74400

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.252

Alfa AF: 0.235 Hom.: 9297

Bravo AF: 0.259

Asia WGS AF: 0.451 AC: 1571 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	0.064
Dann	Benign	0.33

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: rs13150445; hg19: chr4-38931097; COSMIC: COSV62671958; COSMIC: COSV62671958;