chr12-13069572-C-T

Variant names:

• chr12-13069572-C-T
• rs11055225
• NM_020853.2:c.1368+861C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020853.2(FAM234B):​c.1368+861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,030 control chromosomes in the GnomAD database, including 2,166 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 0.12 (2166 hom., cov: 32)
• Consequence: FAM234B NM_020853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM234B	NM_020853.2	c.1368+861C>T		intron_variant	Intron 9 of 12	ENST00000197268.13	NP_065904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM234B	ENST00000197268.13	c.1368+861C>T		intron_variant	Intron 9 of 12	1	NM_020853.2	ENSP00000197268.8
FAM234B	ENST00000537625.1	c.696+861C>T		intron_variant	Intron 6 of 8	1		ENSP00000437974.1
FAM234B	ENST00000416494.6	n.1368+861C>T		intron_variant	Intron 9 of 13	2		ENSP00000394063.2
FAM234B	ENST00000541950.1	n.446+861C>T		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17618 AN: 151912 Hom.: 2161 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.116 AC: 17651 AN: 152030 Hom.: 2166 Cov.: 32 AF XY: 0.118 AC XY: 8736 AN XY: 74316

African (AFR) AF: 0.288 AC: 11942 AN: 41432

American (AMR) AF: 0.0440 AC: 672 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1699 AN: 5158

South Asian (SAS) AF: 0.183 AC: 881 AN: 4802

European-Finnish (FIN) AF: 0.0440 AC: 465 AN: 10576

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1652 AN: 67990

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0656 Hom.: 369

Bravo AF: 0.122

Asia WGS AF: 0.258 AC: 895 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.014
DANN	Benign	0.45
PhyloP100		-3.1
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: rs11055225; hg19: chr12-13222506;