rs2123068

Variant names:

• chr15-32798683-T-G
• rs2123068
• NM_001277313.2:c.4130+121A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-32798683-T-G
• chr15-32798683-T-A
• chr15-32798683-T-C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001277313.2(FMN1):​c.4130+121A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 933,616 control chromosomes in the GnomAD database, including 30,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3999 hom., cov: 32)
  • Exomes 𝑓: 0.25 (26153 hom.)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.104
• Publications: 3 publications found

Genes affected

FMN1 (HGNC:3768): (formin 1) This gene belongs to the formin homology family and encodes a protein that has a role in the formation of adherens junction and the polymerization of linear actin cables. The homologous gene in mouse is associated with limb deformity. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]

LOC107984089 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 15-32798683-T-G is Benign according to our data. Variant chr15-32798683-T-G is described in ClinVar as Benign. ClinVar VariationId is 1294830.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277313.2. 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
	FMN1	NM_001277313.2	MANE Select	c.4130+121A>C		intron	N/A	NP_001264242.1	Q68DA7-1
	FMN1	NM_001103184.4		c.3461+121A>C		intron	N/A	NP_001096654.1	Q68DA7-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	ENST00000616417.5	TSL:5 MANE Select	c.4130+121A>C		intron	N/A	ENSP00000479134.1	Q68DA7-1
	FMN1	ENST00000334528.13	TSL:1	c.3461+121A>C		intron	N/A	ENSP00000333950.9	Q68DA7-5
	FMN1	ENST00000561249.5	TSL:5	c.3836+121A>C		intron	N/A	ENSP00000453443.1	H0YM30

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30637 AN: 152096 Hom.: 3997 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.248 AC: 193688 AN: 781402 Hom.: 26153 AF XY: 0.245 AC XY: 96465 AN XY: 394342

African (AFR) AF: 0.0440 AC: 784 AN: 17802

American (AMR) AF: 0.292 AC: 4971 AN: 17042

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 3878 AN: 15626

East Asian (EAS) AF: 0.0167 AC: 528 AN: 31596

South Asian (SAS) AF: 0.151 AC: 7144 AN: 47306

European-Finnish (FIN) AF: 0.256 AC: 9300 AN: 36280

Middle Eastern (MID) AF: 0.210 AC: 567 AN: 2706

European-Non Finnish (NFE) AF: 0.274 AC: 158019 AN: 576370

Other (OTH) AF: 0.232 AC: 8497 AN: 36674

GnomAD4 genome AF: 0.201 AC: 30641 AN: 152214 Hom.: 3999 Cov.: 32 AF XY: 0.202 AC XY: 15044 AN XY: 74418

African (AFR) AF: 0.0518 AC: 2152 AN: 41546

American (AMR) AF: 0.279 AC: 4263 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.0256 AC: 133 AN: 5188

South Asian (SAS) AF: 0.150 AC: 725 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2712 AN: 10594

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18839 AN: 67980

Other (OTH) AF: 0.195 AC: 413 AN: 2116

Alfa AF: 0.156 Hom.: 344

Bravo AF: 0.196

Asia WGS AF: 0.0860 AC: 302 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.030
DANN	Benign	0.33
PhyloP100		-0.10
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: rs2123068; hg19: chr15-33090884;