2-152618739-A-T

Variant names:

• chr2-152618739-A-T
• rs13413144
• NM_052905.4:c.1315-107A>T

Variant summary

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

The NM_052905.4(FMNL2):​c.1315-107A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 978,424 control chromosomes in the GnomAD database, including 36,135 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 0.20 (3813 hom., cov: 33)
  • Exomes 𝑓: 0.27 (32322 hom.)
• Consequence: FMNL2 NM_052905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 1 publications found

Genes affected

FMNL2 (HGNC:18267): (formin like 2) This gene encodes a formin-related protein. Formin-related proteins have been implicated in morphogenesis, cytokinesis, and cell polarity. Alternatively spliced transcript variants encoding different isoforms have been described but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMNL2	NM_052905.4	c.1315-107A>T		intron_variant	Intron 13 of 25	ENST00000288670.14	NP_443137.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMNL2	ENST00000288670.14	c.1315-107A>T		intron_variant	Intron 13 of 25	1	NM_052905.4	ENSP00000288670.9

Frequencies

GnomAD3 genomes AF: 0.199 AC: 29920 AN: 150362 Hom.: 3814 Cov.: 33

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00837

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.267 AC: 220745 AN: 827944 Hom.: 32322 AF XY: 0.265 AC XY: 109698 AN XY: 414214

African (AFR) AF: 0.0471 AC: 917 AN: 19478

American (AMR) AF: 0.244 AC: 4579 AN: 18752

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 2449 AN: 15476

East Asian (EAS) AF: 0.00528 AC: 179 AN: 33912

South Asian (SAS) AF: 0.221 AC: 10113 AN: 45710

European-Finnish (FIN) AF: 0.213 AC: 9298 AN: 43684

Middle Eastern (MID) AF: 0.148 AC: 431 AN: 2912

European-Non Finnish (NFE) AF: 0.301 AC: 183777 AN: 610086

Other (OTH) AF: 0.237 AC: 9002 AN: 37934

GnomAD4 genome AF: 0.199 AC: 29915 AN: 150480 Hom.: 3813 Cov.: 33 AF XY: 0.193 AC XY: 14184 AN XY: 73574

African (AFR) AF: 0.0573 AC: 2315 AN: 40390

American (AMR) AF: 0.234 AC: 3541 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 502 AN: 3428

East Asian (EAS) AF: 0.00819 AC: 42 AN: 5126

South Asian (SAS) AF: 0.208 AC: 994 AN: 4778

European-Finnish (FIN) AF: 0.197 AC: 2083 AN: 10582

Middle Eastern (MID) AF: 0.123 AC: 35 AN: 284

European-Non Finnish (NFE) AF: 0.293 AC: 19846 AN: 67734

Other (OTH) AF: 0.171 AC: 358 AN: 2088

Alfa AF: 0.237 Hom.: 616

Bravo AF: 0.189

Asia WGS AF: 0.0950 AC: 329 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.021
DANN	Benign	0.39
PhyloP100		-0.82
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: rs13413144; hg19: chr2-153475253;