rs1122794

chr16-259156-C-A

Variant summary

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

The NM_032039.4(FAM234A):c.269-327C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,080 control chromosomes in the GnomAD database, including 2,913 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 0.19 (2913 hom., cov: 32)
• Consequence: FAM234A NM_032039.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM234A	NM_032039.4	c.269-327C>A		intron_variant		ENST00000399932.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM234A	ENST00000399932.8	c.269-327C>A		intron_variant		1	NM_032039.4	P1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29284 AN: 151962 Hom.: 2909 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.193 AC: 29307 AN: 152080 Hom.: 2913 Cov.: 32 AF XY: 0.192 AC XY: 14283 AN XY: 74338

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.199

Alfa AF: 0.190 Hom.: 1327

Bravo AF: 0.196

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.6
Dann	Benign	0.67

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: rs1122794; hg19: chr16-309155;