chr15-32774521-CCCTA-C

Variant names:

• chr15-32774521-CCCTA-C
• rs10540596
• NM_001277313.2:c.4216-171_4216-168delTAGG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001277313.2(FMN1):​c.4216-171_4216-168delTAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,180 control chromosomes in the GnomAD database, including 296 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.052 (296 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.771
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 15-32774521-CCCTA-C is Benign according to our data. Variant chr15-32774521-CCCTA-C is described in ClinVar as Benign. ClinVar VariationId is 1275341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 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.4216-171_4216-168delTAGG		intron	N/A	NP_001264242.1	Q68DA7-1
	FMN1	NM_001103184.4		c.3547-171_3547-168delTAGG		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.4216-171_4216-168delTAGG		intron	N/A	ENSP00000479134.1	Q68DA7-1
	FMN1	ENST00000334528.13	TSL:1	c.3547-171_3547-168delTAGG		intron	N/A	ENSP00000333950.9	Q68DA7-5
	FMN1	ENST00000561249.5	TSL:5	c.3922-171_3922-168delTAGG		intron	N/A	ENSP00000453443.1	H0YM30

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7859 AN: 152062 Hom.: 298 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0516 AC: 7853 AN: 152180 Hom.: 296 Cov.: 32 AF XY: 0.0529 AC XY: 3935 AN XY: 74402

African (AFR) AF: 0.0765 AC: 3177 AN: 41528

American (AMR) AF: 0.0378 AC: 578 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.174 AC: 897 AN: 5148

South Asian (SAS) AF: 0.104 AC: 499 AN: 4806

European-Finnish (FIN) AF: 0.0257 AC: 273 AN: 10608

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0308 AC: 2097 AN: 68008

Other (OTH) AF: 0.0487 AC: 103 AN: 2114

Alfa AF: 0.0406 Hom.: 24

Bravo AF: 0.0529

Asia WGS AF: 0.161 AC: 556 AN: 3478

ClinVar

ClinVar submissions as Germline

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
PhyloP100		0.77
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: rs10540596; hg19: chr15-33066722;