NM_001277313.2:c.*184C>T

Variant names:

• chr15-32774126-G-A
• rs16958710
• NM_001277313.2:c.*184C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001277313.2(FMN1):​c.*184C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 604,430 control chromosomes in the GnomAD database, including 3,951 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (881 hom., cov: 32)
  • Exomes 𝑓: 0.11 (3070 hom.)
• Consequence: FMN1 NM_001277313.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.958
• Publications: 8 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 15-32774126-G-A is Benign according to our data. Variant chr15-32774126-G-A is described in ClinVar as Benign. ClinVar VariationId is 1233503.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 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.*184C>T		3_prime_UTR	Exon 21 of 21	NP_001264242.1	Q68DA7-1
	FMN1	NM_001103184.4		c.*184C>T		3_prime_UTR	Exon 17 of 17	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.*184C>T		3_prime_UTR	Exon 21 of 21	ENSP00000479134.1	Q68DA7-1
	FMN1	ENST00000334528.13	TSL:1	c.*184C>T		3_prime_UTR	Exon 17 of 17	ENSP00000333950.9	Q68DA7-5
	FMN1	ENST00000561249.5	TSL:5	c.*184C>T		downstream_gene	N/A	ENSP00000453443.1	H0YM30

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15745 AN: 152020 Hom.: 881 Cov.: 32

Gnomad AFR AF: 0.0689

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.112 AC: 50752 AN: 452292 Hom.: 3070 Cov.: 4 AF XY: 0.111 AC XY: 27122 AN XY: 243566

African (AFR) AF: 0.0644 AC: 615 AN: 9544

American (AMR) AF: 0.114 AC: 1350 AN: 11834

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 2198 AN: 16204

East Asian (EAS) AF: 0.130 AC: 3359 AN: 25808

South Asian (SAS) AF: 0.0957 AC: 4036 AN: 42182

European-Finnish (FIN) AF: 0.130 AC: 5639 AN: 43424

Middle Eastern (MID) AF: 0.126 AC: 467 AN: 3702

European-Non Finnish (NFE) AF: 0.110 AC: 30137 AN: 273684

Other (OTH) AF: 0.114 AC: 2951 AN: 25910

GnomAD4 genome AF: 0.104 AC: 15755 AN: 152138 Hom.: 881 Cov.: 32 AF XY: 0.104 AC XY: 7769 AN XY: 74368

African (AFR) AF: 0.0689 AC: 2859 AN: 41504

American (AMR) AF: 0.108 AC: 1645 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.130 AC: 672 AN: 5180

South Asian (SAS) AF: 0.110 AC: 528 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1461 AN: 10566

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7746 AN: 68000

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.111 Hom.: 502

Bravo AF: 0.103

Asia WGS AF: 0.118 AC: 408 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.96
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: rs16958710; hg19: chr15-33066327; COSMIC: COSV57922398; COSMIC: COSV57922398;