12-13058782-A-G

Position:

• chr12-13058782-A-G

Variant summary

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

The NM_020853.2(FAM234B):​c.532+233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 152,238 control chromosomes in the GnomAD database, including 642 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 0.063 (642 hom., cov: 32)
• Consequence: FAM234B NM_020853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

FAM234B (HGNC:29288): (family with sequence similarity 234 member B) Predicted to be located in Golgi apparatus and cytoskeleton. Predicted to be integral component of membrane. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM234B	NM_020853.2	c.532+233A>G		intron_variant		ENST00000197268.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM234B	ENST00000197268.13	c.532+233A>G		intron_variant		1	NM_020853.2	P1
FAM234B	ENST00000416494.6	c.532+233A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9647 AN: 152120 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0635 AC: 9660 AN: 152238 Hom.: 642 Cov.: 32 AF XY: 0.0681 AC XY: 5070 AN XY: 74446

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0412 Hom.: 49

Bravo AF: 0.0609

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.64

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: rs10492246; hg19: chr12-13211716;