rs3825271

Positions:

• chr12-13063137-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.852+162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0618 in 152,228 control chromosomes in the GnomAD database, including 629 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 0.062 (629 hom., cov: 32)
• Consequence: FAM234B NM_020853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

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=-0.89).
• 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	Protein	UniProt
FAM234B	NM_020853.2	c.852+162A>G		intron_variant		ENST00000197268.13	NP_065904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM234B	ENST00000197268.13	c.852+162A>G		intron_variant		1	NM_020853.2	ENSP00000197268.8
FAM234B	ENST00000537625.1	c.180+162A>G		intron_variant		1		ENSP00000437974.1
FAM234B	ENST00000416494.6	n.852+162A>G		intron_variant		2		ENSP00000394063.2
FAM234B	ENST00000541950.1	n.220+162A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9394 AN: 152110 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0618 AC: 9407 AN: 152228 Hom.: 629 Cov.: 32 AF XY: 0.0665 AC XY: 4951 AN XY: 74422

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0230 Hom.: 353

Bravo AF: 0.0596

Asia WGS AF: 0.211 AC: 734 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	0.045
DANN	Benign	0.63

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: rs3825271; hg19: chr12-13216071; COSMIC: COSV52197857; COSMIC: COSV52197857;