rs13335629

Positions:

• chr16-260381-G-A
• chr16-260381-G-C

Variant summary

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

The ENST00000399932.8(FAM234A):​c.577+221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 593,928 control chromosomes in the GnomAD database, including 386 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 0.033 (299 hom., cov: 33)
  • Exomes 𝑓: 0.0041 (87 hom.)
• Consequence: FAM234A ENST00000399932.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

FAM234A (HGNC:14163): (family with sequence similarity 234 member A) Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM234A	NM_032039.4	c.577+221G>A		intron_variant		ENST00000399932.8	NP_114428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM234A	ENST00000399932.8	c.577+221G>A		intron_variant		1	NM_032039.4	ENSP00000382814	P1

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4989 AN: 152206 Hom.: 296 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0158

GnomAD3 exomes AF: 0.0108 AC: 768 AN: 71004 Hom.: 44 AF XY: 0.00884 AC XY: 319 AN XY: 36092

Gnomad AFR exome AF: 0.118

Gnomad AMR exome AF: 0.00321

Gnomad ASJ exome AF: 0.000464

Gnomad EAS exome AF: 0.000230

Gnomad SAS exome AF: 0.000742

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000279

Gnomad OTH exome AF: 0.00129

GnomAD4 exome AF: 0.00407 AC: 1797 AN: 441604 Hom.: 87 Cov.: 3 AF XY: 0.00326 AC XY: 759 AN XY: 233078

Gnomad4 AFR exome AF: 0.112

Gnomad4 AMR exome AF: 0.00445

Gnomad4 ASJ exome AF: 0.000887

Gnomad4 EAS exome AF: 0.0000675

Gnomad4 SAS exome AF: 0.000818

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000170

Gnomad4 OTH exome AF: 0.00730

GnomAD4 genome AF: 0.0329 AC: 5009 AN: 152324 Hom.: 299 Cov.: 33 AF XY: 0.0323 AC XY: 2406 AN XY: 74496

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.00922 Hom.: 10

Bravo AF: 0.0371

Asia WGS AF: 0.00924 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.52

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: rs13335629; hg19: chr16-310380;