rs3825271

Variant names:

• chr12-13063137-A-G
• rs3825271
• NM_020853.2:c.852+162A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020853.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234B	NM_020853.2	MANE Select	c.852+162A>G		intron	N/A	NP_065904.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234B	ENST00000197268.13	TSL:1 MANE Select	c.852+162A>G		intron	N/A	ENSP00000197268.8
	FAM234B	ENST00000537625.1	TSL:1	c.180+162A>G		intron	N/A	ENSP00000437974.1
	FAM234B	ENST00000416494.6	TSL:2	n.852+162A>G		intron	N/A	ENSP00000394063.2

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

African (AFR) AF: 0.122 AC: 5068 AN: 41526

American (AMR) AF: 0.0220 AC: 336 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1394 AN: 5174

South Asian (SAS) AF: 0.141 AC: 678 AN: 4816

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 746 AN: 68024

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0302 Hom.: 793

Bravo AF: 0.0596

Asia WGS AF: 0.211 AC: 734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.045
DANN	Benign	0.63
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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