rs3741818

Variant names:

• chr12-13061603-A-G
• rs3741818
• NM_020853.2:c.561A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-13061603-A-G
• chr12-13061603-A-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_020853.2(FAM234B):​c.561A>G​(p.Val187Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 1,612,674 control chromosomes in the GnomAD database, including 542,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.73 (41896 hom., cov: 31)
  • Exomes 𝑓: 0.82 (500694 hom.)
• Consequence: FAM234B NM_020853.2 synonymous
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.859
• Publications: 24 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 12-13061603-A-G is Benign according to our data. Variant chr12-13061603-A-G is described in ClinVar as Benign. ClinVar VariationId is 3060677.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=0.859 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234B	NM_020853.2	MANE Select	c.561A>G	p.Val187Val	synonymous	Exon 4 of 13	NP_065904.1	A2RU67

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM234B	ENST00000197268.13	TSL:1 MANE Select	c.561A>G	p.Val187Val	synonymous	Exon 4 of 13	ENSP00000197268.8	A2RU67
	FAM234B	ENST00000893327.1		c.462A>G	p.Val154Val	synonymous	Exon 3 of 12	ENSP00000563386.1
	FAM234B	ENST00000416494.6	TSL:2	n.561A>G		non_coding_transcript_exon	Exon 4 of 14	ENSP00000394063.2	A2RU67

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110412 AN: 151636 Hom.: 41897 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.748

GnomAD2 exomes AF: 0.745 AC: 186428 AN: 250076 AF XY: 0.757

Gnomad AFR exome AF: 0.510

Gnomad AMR exome AF: 0.620

Gnomad ASJ exome AF: 0.767

Gnomad EAS exome AF: 0.470

Gnomad FIN exome AF: 0.787

Gnomad NFE exome AF: 0.856

Gnomad OTH exome AF: 0.784

GnomAD4 exome AF: 0.823 AC: 1201736 AN: 1460920 Hom.: 500694 Cov.: 43 AF XY: 0.821 AC XY: 596812 AN XY: 726698

African (AFR) AF: 0.513 AC: 17155 AN: 33450

American (AMR) AF: 0.637 AC: 28436 AN: 44624

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 19941 AN: 26126

East Asian (EAS) AF: 0.509 AC: 20199 AN: 39674

South Asian (SAS) AF: 0.730 AC: 62880 AN: 86160

European-Finnish (FIN) AF: 0.791 AC: 42223 AN: 53380

Middle Eastern (MID) AF: 0.787 AC: 4521 AN: 5746

European-Non Finnish (NFE) AF: 0.862 AC: 958276 AN: 1111418

Other (OTH) AF: 0.797 AC: 48105 AN: 60342

GnomAD4 genome AF: 0.728 AC: 110429 AN: 151754 Hom.: 41896 Cov.: 31 AF XY: 0.723 AC XY: 53620 AN XY: 74144

African (AFR) AF: 0.521 AC: 21492 AN: 41264

American (AMR) AF: 0.748 AC: 11397 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2697 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2420 AN: 5124

South Asian (SAS) AF: 0.721 AC: 3468 AN: 4810

European-Finnish (FIN) AF: 0.779 AC: 8212 AN: 10546

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58299 AN: 67998

Other (OTH) AF: 0.748 AC: 1574 AN: 2104

Alfa AF: 0.806 Hom.: 77992

Bravo AF: 0.709

Asia WGS AF: 0.569 AC: 1982 AN: 3478

EpiCase AF: 0.854

EpiControl AF: 0.852

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	FAM234B-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.4
DANN	Benign	0.76
PhyloP100		0.86
PromoterAI		0.022	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3741818; hg19: chr12-13214537; COSMIC: COSV52195016; COSMIC: COSV52195016;